Pro- and anti-Russian protesters have clashed in the Ukraine region of Crimea, as Russia orders battle-readiness checks on armed forces near the nations' borders and says it is moving to ensure the security of its Black Sea fleet.

Scuffles broke out outside the Crimea regional parliament on Wednesday between thousands of pro-Russia separatists and supporters of Ukraine's new leaders as regional politicians prepared to debate the removal of the pro-Russian Viktor Yanukovich from the presidency.

Russian President Vladimir Putin issued battle drills for army, navy and airforce troops based in Russia's western military district, which borders Ukraine, Belarus, the Baltic states, Finland and the Arctic.

Russia's Defence Ministry was later reported by Reuters to have said it was taking measures to ensure the security of its facilities and arsenals of its Ukraine-based Black Sea naval fleet.

"The commander-in-chief has set the task of checking the capability of the armed forces to deal with crisis situations posing a threat to the military security of the country," Sergei Shoigu, defence minister, told Interfax news agency.

Shoigu said that "generally speaking, the drill is not in any way related to the events in Ukraine".

Al Jazeera's Rory Challands, reporting from Moscow, said that similar inspections were made regularly in Russia to ensure readiness.

"The government will be well aware, however, that reminding its neighbours and rivals of Russian military might at this time is not such a bad thing to be doing." he said.

Separately to the Russian announcement, the secretary general of NATO, Anders Fogh Rasmussen, said the alliance to "for granted that all nations respect the sovereignty ... and territorial integrity of Ukraine".

"This is a message that we have also conveyed to whom it may concern," he said, without naming Russia.

The US urged Russia to keep its word to respect the territorial integrity of Ukraine and warned against provocative actions after Russia said it was boosting security measures in southern Crimea.

"We are making it clear that every country should respect the territorial integrity here, the sovereignty of Ukraine. Russia said it will do that, and we think it is important Russia keeps its word," Kerry said.

About 2,000 people, many of them ethnic Tatars who are the indigenous group on the Black Sea peninsula, converged on the parliament building on Wednesday to support the "Euromaidan" movement which overturned Yanukovich in Kiev after three months of protests.

They were met by a similar number of pro-Russia demonstrators who bellowed loyalty to Moscow and denounced the "bandits" who had seized power in Kiev.

The two sides, who were held apart by police lines, rallied outside the parliament which, under pressure from pro-Russia forces, had called an emergency session for later on Wednesday to discuss the crisis.

Crimea was transferred from Russia to Ukraine in 1954 in the Soviet-era by then Soviet leader Nikita Khrushchev.

With a part of Russia's Black Sea fleet based in the port of Sevastopol, it is the only region of Ukraine where ethnic Russians dominate in numbers, although many ethnic Ukrainians in other eastern areas speak Russian as their first language.

With Crimea now the last big bastion of opposition to the new post-Yanukovich political order in Kiev, Ukraine's new leaders are voicing alarm over signs of separatism there.

Since Yanukovich's downfall, all eyes have been on Putin, who in 2008 ordered an invasion of Georgia to protect self-declared independent regions of Abkhazia and South Ossetia with many ethnic Russians, which he then recognised as independent states.

In Kiev on Wednesday, Ukraine's protest leaders named Arseny Yatseniuk, a former economy minister, as a candidate to head a new government following the overthrow of President Viktor Yanukovich.

The Euromaidan council made its announcement of Yatseniuk, plus candidates for several other key ministers, after its members addressed crowds on Kiev's Independence Square.

Al Jazeera's Tim Friend, reporting from Kiev, said that potential candidates for government were being brought on stage to "cheers and jeers" from the crowd as people gauged the audience's reaction.