The embattled government in Kiev said Monday night that Russian forces had dramatically escalated the standoff between the two nations by giving Ukraine’s army and navy in Crimea a blunt ultimatum: Pledge allegiance to the region’s new pro-Russia leadership or be forced by Russia to submit.

A spokesman for the Russian Black Sea Fleet, which is berthed in the Crimean port of Sevastopol, denied that a threat had been made, and the Russian Defense Ministry called the accusation “utter nonsense.” But as Russian troops and warships surrounded Ukrainian security installations throughout the autonomous Crimean Peninsula, it was clear that Ukrainian forces believed they faced an imminent threat.

Early Tuesday, in a sign that he might be trying to diffuse tensions, or that he has accomplished what he wants in Crimea, Russian President Vladimir Putin ordered troops conducting military exercises near Ukraine in Western Russia to return to their bases, according to Russian news agencies. The military exercises were scheduled to end today.

The standoff in Crimea continued.

There were several reports that a pro-Russian fighter who had taken control of an air base in Crimea fired a warning shot into the air Tuesday as Ukrainian soldiers returned to demand their jobs back at the Belbek airport.

A Ukrainian Defense Ministry official alleged that Russia’s Black Sea Fleet commander had set a deadline of 5 a.m. Tuesday — 10 p.m. Monday Eastern time — for Ukrainian forces to capitulate, according to the Interfax-Ukrainian news agency. There were no immediate reports of activity after the deadline passed.

The stepped-up Russian troop movements came two days after Russia’s parliament approved the use of force to protect the country’s citizens and military sites in Crimea, a region with deep ties to Russia. The actions on Monday triggered a cascade of condemnation from European and American officials, who vowed that Russia would face consequences if it did not pull back its soldiers.

President Obama said Moscow was “on the wrong side of history” and threatened “a whole series of steps — economic, diplomatic — that will isolate Russia and will have a negative impact on Russia’s economy and its status in the world.”

Here in the deep-water harbor at Sevastopol, a Ukrainian naval command ship was confronted Monday evening by four tugboats flying Russian colors and was boxed in by a Russian minesweeper. Other Russian warships appeared at the mouth of the harbor to block an escape to the sea. A nearby Ukrainian naval station flew a Russian flag.

As the anxious wives of officers on the Ukrainian ship watched from shore, its crew rushed about in what appeared to be an attempt to repel potential boarders. The sailors — who carried side arms and military assault rifles — fixed mattresses to the railings, uncoiled fire hoses and brought firefighting equipment on deck.

On Monday night, the Russian Black Sea Fleet ordered the crew members to lay down their arms and leave the ships, according to the UNIAN news agency, quoting a Ukrainian military source.

Ukrainian officials expressed fears that the tensions could lead to violence overnight, which could give Russia reason to justify military action.

“Provocations with killing of three to four Russian soldiers are planned on the territory of Crimea tonight,” said Ukrainian Deputy Interior Minister Mykola Velichkovych, the ministry’s press service reported. Speaking to the Russians, Velichkovych said: “We call on you to come to your senses. We call on you to stop.”

Ukraine’s acting president, Oleksandr Turchynov, said Monday that he had been in communication with Ukraine’s military commanders in Crimea and that they assured him they would not yield to the Russians, according to the UNN news agency of Ukraine.

Western diplomats pressed Russia to pull back. In an interview with the BBC, British Foreign Secretary William Hague, who was in Kiev, said the Russian intervention in Crimea has produced “a very tense and dangerous situation” that amounts to Europe’s “biggest crisis” in the 21st century.

“The world cannot just allow this to happen,” said Hague, whose American counterpart, Secretary of State John F. Kerry, was due in Kiev on Tuesday.

French Foreign Minister ­Laurent Fabius said the European Union would have an emergency summit Thursday and take action against Russia if it has not sent troops back to their barracks in the Crimea by then.

But the Western threats appeared to have made little impact on Russia by Monday night. Speaking in Geneva, Russian Foreign Minister Sergei Lavrov justified the Russian troop deployment as necessary to protect Russians living in Crimea “until the normalization of the political situation” in Ukraine, where months of protests led to the ouster of pro-Russian President Viktor Yanukovych last month.

Russian forces, already in control of much of Crimea, took possession of a ferry terminal in Kerch, in the eastern part of the peninsula just across a strait from Russian territory, according to reports from the area. The terminal serves as a departure point for many ships headed to Russia and could be used to send more Russian troops into Crimea.

Ukrainian news media reported that a representative of Russia’s Black Sea Fleet also called on members of Ukraine’s Aviation Brigade at an air base in Belbek to denounce the Ukrainian government’s authority and swear allegiance to the new Crimean government. By nightfall, the Ukrainian aviators were still on their base.

In the capital, Ukraine’s interim prime minister, Arseniy Yatsenyuk, urged the West to provide political and economic support as the Kiev stock market dropped a record 12 percent and the Ukrainian hryvnia fell to new lows against the dollar and euro. The crisis also caused the Moscow market to fall 10 percent and the Russian ruble to dive.

Yatsenyuk stressed that Crimea remained part of Ukraine, but he conceded that there were “for today, no military options on the table.”

Obama administration officials said Russia now has 6,000 troops in Crimea. Ukraine’s ambassador to the United Nations said Monday that 16,000 additional Russian troops had been deployed to Crimea in the past six days. Military experts estimate that the size of the Ukrainian military in Crimea is about 30,000, but many of those are support staff.

Ukraine’s military, at an estimated 130,000 troops, is a considerably larger force than the small and poorly armed Georgian military that the Russians were able to intimidate in 2008, when those two countries went to war over breakaway territory.

[Read: Why the situation in Crimea is different from the Georgia-Russia crisis in 2008.]

But while Ukrainian troops have held firm and refused to open their gates, they are in an increasingly precarious position, “with no way out and no one to rescue them,” a specialist on military affairs in Eurasia said, speaking on the condition of anonymity because he is prohibited by his employer from talking to the news media without permission.

“The Russian troops surrounding them are clearly well-trained special forces, well-disciplined enough that they managed to box up the Ukrainian forces without firing a shot,” the specialist said.

But some military experts said that despite appearances, they doubt that Russia is eager for a fight that might carry a steep price. Even in eastern Ukraine, where Russian is the predominant language, an incursion by Moscow could unify the divided country, said Dmitry Gorenburg, a senior research scientist at the Center for Naval Analyses in Alexandria, Va.

“They are certainly more pro-Russian and Russian speaking” in the east, he said, “but that doesn’t mean that they don’t have a Ukrainian national identity, especially when they are attacked. It is hard to imagine a course of action on the part of Russia that could have done more to unify Ukraine than what has been done.”

The Ukrainian military has no obvious fault lines, no ethnic or regional differences, that might make it vulnerable to defection and dissension.

At the same time, individual loyalties are unknown. If Yanukovych were to appoint himself head of a government in exile, he might be able to call in old favors from among officers. Like other institutions in Ukraine, the military has been beset by corruption, which could mean officers might be beholden to people other than their superiors.

In Sevastopol, a Ukrainian admiral who defected to the side of the pro-
Russian Crimean government tried to persuade his fellow officers in a meeting Monday morning to join him. They refused.

As they did in Sunday’s standoff at a Ukrainian army base in Perevalne, armed Russian troops, demonstrating who was in charge, posted guards at the gates of the Ukraine naval station in Sevastopol as Ukrainian marines appeared to be trapped inside the base.

Englund reported from Kiev. Kathy Lally in Moscow and Greg Jaffe in Washington contributed to this report.