A dozen Russian soldiers at the Belbek base warned the unarmed Ukrainian men not to approach before firing the warning shots and reportedly threatening to shoot if the men marched any closer towards them.
Meanwhile, Russian president Vladimir Putin described the ousting of the Ukrainian former president as “an anti-constitutional overthrow and armed seizure of power” in his first press conference since the crisis began.
He said there was currently no need to send Russian troops into Ukraine yet, but said: "What we are seeing in Ukraine is not an expression of democracy".
Despite blunt warnings about costs and consequences, President Barack Obama and European leaders have limited options for retaliating against Russia's military intervention in Ukraine, the former Soviet republic now at the center of an emerging conflict between East and West
He said there was only three ways a president can leave power in Ukraine - through death, resignation, or impeachment. Therefore, he said, Mr Yanukovych, from a legal perspective, is still the legitimate president.
The US has now announced it will suspend all military co-operations with Moscow, over its intervention in Ukraine. Pentagon spokesman Rear Admiral John Kirby has said all military exercises, port visits, bilateral talks and planning conferences between Russia and the US are being put on hold.
The warning shots came after the 3am deadline Russia allegedly gave Ukrainian forces as the time they must leave Crimea by or face a military attack expired without incident.
Russian news agencies reported this morning that Mr Putin had ordered his troops on military exercises near the border between western Russia and Ukraine to return to bases after completing all of their tasks.
A statement by Russian presidential spokesman Dmitry Peskov said that manoeuvres had been "a success".
Two Ukrainian warships remained anchored in the Crimean port of Sevastopol early this morning, a day after authorities claimed Russian forces had issued an ultimatum for the ships to surrender or be seized.
Russia had earlier rejected reports of the surrender ultimatum as "total nonsense". It said troops went in following a written request by the ousted president Viktor Yanukovych to protect civilians.
According to a deputy commander at one of Ukraine's units in Crimea there were no attempts to storm the base. The commander, named only as Major Lisovoy, told local TV station ATR: "We're all in high spirits, ready to defend our base. There was no official ultimatum, it was done indirectly via mobile phones. I want peace and stability and for Ukraine to be a united country."
Russian troops said by Ukraine’s ambassador to be 16,000 strong tightened their grip on Ukraine's Crimean Peninsula yesterday.
Soldiers controlled all Crimean border posts, as well as military facilities in the territory and a ferry terminal in the city of Kerch, just 20 kilometers (12 miles) across the water from Russia.
The news came as the Ukrainian parliament ratified an agreement to receive €610million (£500million) in loans. The loan was agreed in 2013 but never ratified under Mr Yanukovych.
The US Secretary of State John Kerry will today be reinforcing Washington's support for the new government in Kiev, as America and its top allies grapple with whether to impose sanctions upon Moscow for its military takeover of Crimea.
Mr Kerry is due to arrive soon in Kiev. The European Union's foreign ministers, meanwhile, issued a Thursday deadline for Mr Putin to pull back his troops or face a rejection of visa liberalisation and economic cooperation negotiations long in the works.
Western leaders point to the huge hits Russia's natural gas, uranium and coal industries would take if sanctions cut off exports to the EU, its largest customer.
But Western governments have acknowledged that few options exist beyond economic and diplomatic penalties, and critics said efforts by the Obama administration are too little, and too late, after years of trying to foster friendlier relations with Russia.
President Barack Obama yesterday described the Russian advance as a violation of international law. He called on Congress to approve an aid package for the new Ukrainian government and repeated earlier threats that the US will take steps to hobble Russia's economy and isolate it diplomatically if Mr Putin does not back down.
"The strong condemnation that has proceeded from countries around the world indicates the degree to which Russia is on the wrong side of history," Obama said.
The White House said Obama met for more than two hours last night with the National Security Council, including Mr Kerry and Defence Secretary Chuck Hagel, to discuss what steps the United States can take with international partners to prevent the situation from escalating further.
The Pentagon announced late on Monday it was suspending military-to-military engagements with Russia, including exercises, bilateral meetings, port visits and conferences. A senior US official said the US also would not move forward with meetings designed to deepen the trade relationship with Russia.
Speaking at a UN session in Geneva, Russian Foreign Minister Sergey Lavrov defended the deployment of Russian troops in Ukraine as a necessary protection for his country's citizens living there.
"Those who are trying to interpret the situation as a sort of aggression and threatening us with sanctions and boycotts, these are the same partners who have been consistently and vigorously encouraging the political powers close to them to declare ultimatums and renounce dialogue," Mr Lavrov said.
"This is a question of defending our citizens and compatriots, ensuring human rights, especially the right to life," he said.
Lavrov said Ukraine should return to a 21 February agreement that sought to end months of unrest in Kiev by addressing an array of issues at the heart of the dispute between protesters and the government.
US officials say the 21 February agreement could form the "basis" for a political resolution to the crisis, but not in its present form.
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