Ukraine is planning to withdraw its forces and their families from Crimea "quickly and efficiently" after more Ukrainian bases were taken over by local militias and Russian troops on Wednesday.

Andriy Parubiy, head of the national security and defence council, told reporters in Kiev that it planned to relocate 25,000 service personnel and families. "We are developing a plan that would enable us not only to withdraw servicemen but also members of their families in Crimea, so that they could be quickly and efficiently moved to mainland Ukraine."

His comments came before Russian forces took over a naval base in Bakhchisaray in Crimea on Wednesday night, the latest in a series of takeovers of Ukrainian bases by Russian troops and local self-defence forces using a mixture of attrition and threats, as well as the dawning realisation that Kiev has lost control over the peninsula and has no way of fighting to regain it.

On Wednesday, the day after Vladimir Putin announced that Russia would absorb Crimea and a Ukrainian soldier was shot dead by a sniper at a base in Simferopol, a pro-Russian militia took control of the Ukrainian naval headquarters in Sevastopol.

"We freed the prisoners inside this base. This is Russian territory. Moscow already accepted Crimea," said Vladimir Melnik, head of a local self-defence unit, shortly after the Russian flag was raised at the base.

According to Melnik, several branches of the local militia co-ordinated in storming of the site during the morning. "We are peaceful people, but we are military people and if we receive orders to storm we will follow them," he said, adding that the civil defence units were under the command of the city administration.

Andrey Kochebarov, a deputy leader of local Cossacks, said: "There was no fight, no resistance; the guys inside clearly understood what situation they are in. This is the naval base headquarters so if they gave up this one, they will give them all up."

In the hours that followed, the Ukrainian troops, who had been inside the besieged base for three weeks, slowly trickled out with heads bowed. Morale is low and the soldiers say they are uncertain what the future holds.

"We have no word from Kiev about what to do next," said Sergei, who has served as an officer in the Ukrainian army for 21 years and remained inside the building until the bitter end. "Of course, there was no resistance [when the building was stormed]. What are we meant to do, outnumbered and without weapons?" Sergei denied the local militia's claims that the men inside were liberated: "This is a lie. We remained there of our own free will."

Sergei, from Sevastopol, said he and the 50 colleagues who remained inside had been able to leave the building, but would not have been able to return if they did so. "I stayed because I swore an oath to the Ukrainian army." He said the Ukrainian officers were not physically threatened, but they were kept without enough food and water, and the electricity was often shut off.

Outside, his tearful wife greeted him with a hug. "It's been a very difficult time. I was very anxious about his safety," she said. "I'm delighted to have him back."

Tough decisions lie ahead for all the troops in the Crimea region who have remained loyal to Ukraine. Russian and Crimean officials have issued an ultimatum to the Ukrainian troops either to join the Russian army or take the option of a safe passage out of the peninsula.

Parubiy said the Ukrainian government would appeal to the UN to declare Crimea a de-militarised zone, which he hoped would lead to Russia and Ukraine both withdrawing its forces.

The Ukrainian navy commander, Serhiy Haiduk, was captured during the storming of the headquarters and was believed to have been taken into Russian detention. On Wednesday evening, acting Ukrainian president Oleksandr Turchynov gave the Russians and Crimean authorities three hours to free Haiduk or face "adequate responses, including of a technical and technological nature", without clarifying further.

There was no immediate time frame given for Parubiy's announcement that the troops would be relocated.

Ukrainian politician Vitali Klitschko had earlier said Ukraine should not recognise Russian rule over Crimea, but did call for safe passage to be granted so Ukrainian troops on the peninsula could withdraw to "temporary bases" elsewhere in Ukraine, to prevent further bloodshed.

The Ukrainian government wanted to dispatch two ministers to Crimea on Wednesday to "resolve the situation", but were informed by Crimean authorities that they would not be allowed to enter the territory.

The process of annexation continued apace, with Ukrainian signs being removed from government buildings. Russia's constitutional court reviewed the treaty to join Crimea to Russia and found it legal, and the parliament is expected to ratify the decision by the end of the week.

Putin announced that a rail and road bridge connecting the Crimean peninsula to Russia across the two-mile Kerch Strait would be built.

Russia had already begun distributing passports in the region, said Konstantin Romodanovsky, head of Russia's federal migration service. "Some passports were issued today, and the work will only get more intensive with each new day," he told RIA Novosti. He did not clarify what would happen with those Crimea residents who did not take up Russian citizenship.

Concerns have been voiced about the fate of Crimean Tatars, who make up 13% of the population and, on the whole, are loyal to Kiev. They mostly boycotted the hastily organised referendum that returned a 97% vote for union with Russia. Crimean officials have said some of them may have to return land to which they do not own proper legal rights. Many Tatars live on unregistered land; they were deported en masse during the Stalin era and often found their property in new hands when they returned a generation later.

The most pressing issue remains what happens with the remaining Ukrainian servicemen in bases. Crimean authorities claimed that the officer who was shot dead on Tuesday was shot by a 17-year-old radical Ukrainian nationalist, which has been dismissed as implausible by authorities in Kiev.

A spokesperson for the defence ministry was unable to clarify how many soldiers were left on bases, saying he did not know himself. But there was little fighting talk at bases around the peninsula and more of a sense of resignation that the territory has been lost.

Evgeniy Cherednichenko, an officer at the logistical command centre in Sevastopol, on Wednesday made the decision to abandon his position inside the besieged base.

"It's a very difficult and complicated situation. We don't have proper information. In the end, I just decided to pick up my personal stuff and leave," he said. "I have not deserted the Ukrainian army, I don't know what to do next."

The base is surrounded by Russian troops; through the wire fence it is possible to see the Ukrainian troops moving around. A sniper sits calmly on top of a garage watching the men below.

Speaking by telephone from inside the base, lieutenant colonel Aleksandr Lusyan said: "Kiev should have given the order to use weapons at the beginning, because then we could fight back, but they were afraid to give this command because they were afraid to spill blood. Now we are outnumbered and we cannot fight back."