A Kremlin statement said the order was “guided by universally recognised principles and standards of international humanitarian law and in order to protect the rights and freedoms of individuals”.
It gives birth, marriage and death certificates, identification, qualification, vehicle registration certificates and other documents issued by pro-Russian rebel “authorities” official recognition in Russia.
Sergey Lavrov, the Russian foreign minister, claimed the recognition was afforded so “Donbass residents” can enter Russia legally, with thousands already fleeing over the border as asylum seekers.
Mr Putin’s order was released hours after the American Vice President told an international conference the US would “hold Russia accountable” for its actions.
Donald Trump made a series of warm statements towards Mr Putin during his campaign and has dismissed allegations of Russian interference in the election, but has adopted a more combative tone in recent days following international pressure over Ukraine.
The President accused Russia of using force to “take” Crimea, which it annexed from Ukraine in 2014, last week amid a fresh round of allegations over links between his administration and the Kremlin.
The Russian foreign ministry responded by calling the Black Sea peninsula “our territory” and declaring that it would not be returned.
Petro Poroshenko, the President of Ukraine, warned against any move to “appease” Russia on the issue.
“I hear increasingly obsessive calls for at least some degree of appeasement toward Russia’s appetite,” he said.
“To move in that direction would be naive, wrong and dangerous — not only for Ukraine, but also for Europe and for the world.”
Mr Putin’s latest order will be seen as another sign to the world that despite its repeated denials of backing Ukrainian rebels, it will not lessen its political support.
A Kremlin statement said it related to “certain districts of Ukraine’s Donetsk and Luhansk”, without specifically referring to the so-called People’s Republics installed on the Russian border during the Ukrainian civil war.
They emerged after months of fighting between separatist rebels and the Ukrainian government following the ousting of President Viktor Yanukovych, an ally of Mr Putin’s.
Russia has denied persistent allegations by Nato and the US and EU of arming rebels and sending its troops over the border, but has made no secret of its political backing for the Donbass “republics”.
They were created after referendums held in May 2014 that claimed to show strong support for independence in Donetsk and Luhansk, although no government officially recognised the result amid evidence of widespread fraud and voter intimidation.
The ongoing conflict, which has intensified in recent weeks, was a hot topic at the annual Munich Security Conference yesterday.
Mike Pence said the Trump administration would demand that Russia honours a 2015 peace deal agreed in Minsk, in efforts to end fighting in eastern Ukraine, which has been repeatedly violated by both sides.
“Know this: The United States will continue to hold Russia accountable, even as we search for new common ground, which as you know President Trump believes can be found,” the Vice President said.
Russian military activity in Crimea
Russian military activity in Crimea
Russian, right, and Ukrainian navy sailors are deployed outside a Ukrainian Coast Guard base in Balaklava near Sevastopol, Crimea (AP)
An unidentified armed man patrols a square in front of the airport in Simferopol, Ukraine (AP)
A soldier rests atop a Russian armored personnel carriers with a road sign reading "Sevastopol - 32 kilometers, Yalta - 70 kilometers", near the town of Bakhchisarai, Ukraine (AP)
Armed Russian navy servicemen surround a Ukrainian border guard base in Balaclava, in the Crimea region (Reuters)
Unidentified soldiers block a road to Ukrainian military airport Belbek not far from Sevastopol (AFP/Getty Images)
Sea gulls perch onboard a Russian military vessel anchored at a navy base in the Ukrainian Black Sea port of Sevastopol (Reuters)
Activists of the Russian Bloc party guard the road to Ukrainian military airport Belbek not far from Sevastopol (AFP/Getty Images)
Ukrainian police walk near the Crimean parliament building in Simferopol. Ukraine said on Thursday it would regard any movements by Russian military in Crimea outside the Russian Black Sea fleet's base in Sevastopol as an act of aggression. (Reuters)
Armed Russian navy servicemen surround a Ukrainian border guard base in Balaclava, in Crimea region (Reuters)
An unidentified gunman holds his assault rifle ready while he and others block the road toward the military airport at the Black Sea port of Sevastopol in Crimea (AP)
A local resident smiles preventing people from going too close to unidentified gunmen blocking the road toward the military airport at the Black Sea port of Sevastopol in Crimea (AP)
The Russian foreign minister hit back by accusing Nato of Cold War-era expansionism and blaming the alliance for rising tensions and military deployments in Europe.
He later announced a fresh ceasefire brokered by Russian, Ukrainian, German and French negotiators to halt fighting between Kiev’s army and rebels from 20 February.
“On 20 February the ceasefire regime will start, and withdrawal of heavy military hardware will also start…failure should not be allowed to take place,” Mr Lavrov told reporters.
But the Ukrainian foreign minister, Pavlo Klimkin, said he was “not at all” happy with the result of talks.
Ukraine’s government has raised concern over an upsurge in fighting over the past month, seeing heavy artillery banned under the Minsk agreements hit residential areas including the frontline city of Avdiivka.
Thousands of people were left without electricity and water because of the battles, which saw rockets kill civilians attempting to shelter in their homes
The Ukrainian embassy in London describes rebels as “Russian terrorist forces”, while the separatists and Russian media frequently refer to government troops as “Nazis”.
Both sides accuse each other of ceasefire violations and war crimes in the conflict, which has killed more than 9,800 people since April 2014.
Additional reporting by agencies