The government of Ukraine, pushing to oust pro-Russian rebels from their last enclaves in the east while nervously eyeing a stalled Russian aid convoy, said on Friday that its force had destroyed a number of Russian military vehicles that it said crossed into Ukraine late Thursday through a border area controlled by the separatists.

Russia denied sending a military column into Ukraine, but the incursion, first reported by British journalists who said they saw 23 armored vehicles crossing the frontier, was confirmed Friday by NATO’s secretary general, Anders Fogh Rasmussen.

“I can confirm that last night we saw a Russian incursion, crossing of the Ukrainian border,” Mr. Rasmussen told journalists during a visit to Copenhagen, according to news agency reports. He did not elaborate on what had happened to the Russian vehicles.

But a statement on the website of Ukraine’s president, Petro O. Poroshenko, said that most of the Russian vehicles had been destroyed. The statement said Mr. Poroshenko had spoken by telephone with Prime Minister David Cameron of Britain about news media reports of a Russian military incursion and told him that “the given information was trustworthy and confirmed because the majority of the machines had been eliminated by Ukrainian artillery at night.” It gave no details.

Ukraine has repeatedly accused Moscow of sending weapons and military hardware to support rebels in eastern Ukraine, including the surface-to-air missile system that Ukraine and its Western supporters believe shot down Malaysia Airlines Flight 17 over rebel-held territory last month.

But the latest reports of Russian armor crossing the border stirred particular alarm amid heightened suspicions over Russia’s intentions after its announcement this week that it was sending a huge convoy of trucks to Ukraine to deliver aid to civilians caught in the conflict zone.

Ukraine has voiced concerns that the aid convoy, now parked in a field inside Russia, could be a cover for a stealthy military intervention like the one in which Russia seized Crimea from Ukraine in March through the covert deployment of heavily armed masked men.

Ukraine’s military spokesman, Andriy Lysenko, told a briefing in Kiev that a large portion of the armored column that passed into Ukraine late Thursday “no longer existed” after a strike by Ukrainian forces. He said Ukraine could not stop Russia sending military material through a rebel-controlled border zone and had adopted a strategy of “allowing the columns deeper into Ukrainian territory where they can be destroyed.”

Mr. Lysenko did not say, however, whether the vehicles were still under Russian control at the time of their destruction, or whether they had already been transferred to the rebels.

The new spike in tensions between Moscow and Kiev came as European Union foreign ministers held an emergency meeting in Brussels on Iraq and Ukraine. Germany’s foreign minister, Frank-Walter Steinmeier, told reporters there that he had spoken to his Russian counterpart, Sergey V. Lavrov, early Friday as diplomats scrambled to establish whether the Russians had moved across the Ukrainian border in some significant fashion linked to the aid convoy rather than “the unfortunately all too frequent movement across the border” that he said can be observed many nights.

European foreign ministers did not announce or threaten any new round of sanctions against Russia, but they issued a tough warning to the Kremlin against trying to use humanitarian aid as a pretext for military action.

“Any unilateral military actions on the part of the Russian Federation in Ukraine under any pretext, including humanitarian, will be considered by the European Union as a blatant violation of international law,” a statement issued at the end of the Brussels meeting said. “In order to achieve rapid and tangible results in de-escalation and to improve the situation of the civilian population, the European Union urges the Russian Federation to put an immediate stop to any form of border hostilities, in particular to the flow of arms, military advisers and armed personnel into the conflict region, and to withdraw its forces from the border.”

Russian news agencies quoted an unidentified spokesman for the Border Guard Service as denying that any Russian vehicles had crossed the border into Ukraine. Such reports, he said, are “completely untrue.”

He said that the Russian border service, run by the domestic intelligence agency, the F.S.B., had simply deployed more mobile teams near the border to counter what he said was increased infiltration by Ukrainian forces into Russia and more frequent shelling across the border.

A reporter for The Guardian said he and a colleague had seen 23 Russian armored personnel carriers, supported by fuel trucks and other vehicles, crossing into Ukraine on Thursday evening through a hole in a barbed-wire fence that used to mark the frontier.

In a sign of the suspicions dividing Moscow and Kiev, the Russian Foreign Ministry accused Ukraine of both stalling the Russian aid convoy and plotting military means to thwart it. The convoy has been idling since Thursday near a Russian military base outside the Russian town of Kamensk-Shakhtinsky because of a dispute over paperwork.

Ukraine has sent more than 50 border guards and customs officials to Russia to inspect the convoy’s cargo, but said they have not been able to start examining the trucks because they have not received necessary documentation from the International Committee of the Red Cross. The Red Cross, for its part, said Russia had yet to provide a detailed inventory and the organization called for a speedy resolution of the problem.

The Russian Foreign Ministry statement accused Ukraine of trying to wreck Russia’s humanitarian efforts, but it did not address the question of whether Moscow had provided a detailed inventory of the trucks’ contents as requested by the Red Cross. The exact nature of the convoy’s cargo has bedeviled Russia’s relief effort from the start because of Ukrainian fears that it could include military aid for pro-Russian separatist rebels.

The statement said intensified Ukrainian government military activity in southeast Ukraine was “obviously” aimed at cutting the planned route of the convoy to Luhansk, and it spoke of a possible attack on the convoy itself. Ukrainian forces on Thursday seized a village that straddles the main road from Russia to Luhansk, a rebel-held Ukrainian city that is the planned destination of the Russian relief supplies.

Roughly 20 minutes after that statement, the Russian ministry issued another one, saying the two sides were working to resolve their differences.

Pavlo Klimkin, the Ukrainian foreign minister, telephoned his Russian counterpart, Mr. Lavrov, and the two agreed on the need for “more urgent” participation of international organizations in completing the humanitarian mission, the brief, second Russian statement said.

By late Friday, it was still not clear when the aid convoy might be cleared for the final leg of its mission.

In a statement issued in Geneva, the Red Cross said swift action was needed to allow “confirmation of the strictly humanitarian nature of the cargo” before the trucks could proceed.

“As and when agreement is reached, we plan to deliver this humanitarian aid to people affected by conflict in eastern Ukraine, health facilities and other welfare organizations,” Laurent Corbaz, the Red Cross’s head of operations for Europe and Central Asia, said during a visit to Kiev. “People are struggling to cope with limited access to basic services such as water and electricity, so speed is of the essence.”

The Ukrainian government, stung by accusations that it is stalling the delivery of Russian relief supplies to the eastern city of Luhansk and is not doing enough to improve the plight of residents caught up in the fighting, is sending its own aid convoys to the besieged city. Mr. Lysenko said 71 Ukrainian trucks had been sent to the conflict zone with food, water, tea, soap and other supplies. He said 390 tons of Ukrainian aid had already arrived in Luhansk.