Vladimir Putin has given the strongest indication yet that Russia is defusing its policy towards Ukraine, saying that Moscow will "respect the choice of the Ukrainian people" and work with the country's government after a new president is elected on Sunday.

Previously, the Kremlin had not made it clear whether it would recognise the vote amid the continuing violence in the east of the country, where pro-Moscow separatists have declared two independent statelets after questionable referendums held earlier this month.

The separatist authorities have said they will do everything possible to disrupt the elections, stating they do not plan to hold "the presidential elections of a neighbouring state" on their territory, and there has been a campaign of terror and intimidation against polling stations and election officials.

Putin blamed the west for provoking the Ukraine crisis and said the country was now experiencing "full-blown civil war". However, he suggested on Friday that the Kremlin would recognise the vote. Since former president Viktor Yanukovych fled Ukraine in February, Moscow has referred to the interim government as a "junta" with no legitimacy. Russia has annexed the Crimea peninsula, and Kiev has accused it of stirring up an armed revolt in the east of the country as well.

As Sunday's election approaches, violence in the east has continued, with Ukraine's defense ministry saying up to 500 insurgents attacked government troops in one clash in eastern Ukraine that left 20 insurgents dead. The ministry said in a statement the clash took place on Thursday as a convoy of Ukrainian troops was attacked outside the eastern village of Rubizhne. Up to 16 Ukrainian soldiers also died on Thursday in an assault on a checkpoint by separatists.

On Friday, the Donbass paramilitary group, which operates with the tacit backing of Kiev, said it had been ambushed by separatist forces, with at least one dead, and many injured or taken hostage.

Voting in the east will be severely limited on Sunday, with pro-Kiev forces not fully in control of the region and a fear that violence could spike as the separatists attempt to disrupt the vote. Kiev has said it will halt its "anti-terrorism operation" against separatist forces on voting day.

Alexander Ivanov, of the Committee of Voters of Ukraine, a non-governmental group monitoring election preparation, expected up to one-third of polling stations to open in Donetsk region. The coordinating groups were meeting in secret, he said, and there were worries there could be attacks on polling stations, or that groups of separatists might try to seize the official result papers at the end of the day.

Russian president Vladimir Putin at the St Petersburg International Economic Forum. Photograph: Mikhail Klimentyev/Ria Novosti/Kremlin Pool/EPA

"Most of the election committees are now meeting underground, and there have been a lot of kidnappings and threats," he said. "These are elections being carried out in conditions of a partisan fight."

Most of the election officials who have been kidnapped have been released shortly afterwards, but the intimidation has worked, said Ivanov, scaring off many others. Almost all the regional election committees have been stormed by armed men, who in many cases have made away with voter lists and the official electoral stamps.

In the west of Donetsk region, where paramilitary groups have helped to reinstall pro-Kiev authorities, the vote will go ahead as normal.

In the region of Velyko Novosilka, officials said the election would proceed as normal, and that all the polling stations would work.

"People were scared after being subject to psychological pressure and phone calls, and many people did not want to take part, but we have found new people and we will ensure that all the stations open," said the new head of the regional administration, Alexander Arykh.

Frontrunner Petro Poroshenko needs more than 50% to win the election in the first round, otherwise there will be a run-off three weeks later. Pro-Kiev authorities in the east are hoping for a first-round victory to avoid another period of political uncertainty. Poroshenko has said he would negotiate with political forces from the east of the country, but not with armed separatists responsible for attacks on official buildings and soldiers.