The MoD said it believed Mr Putin could use a scheduled address to the Duma – the Russian parliament – in three days time to announce that four regions will formally become part of Russia.
The fears were raised as Europe looked to investigate leaks in the controversial Nord Stream 2 pipeline running under the Baltic Sea near Sweden and Denmark. Denmark set up a five mile prohibitive zone around the area to protect ships.
The move came as the Office of the High Commissioner for Human Rights (OHCHR) warned the Russian invasion of Ukraine had created a “dire human rights situation”.
In a report published on Tuesday, the OHCHR said there had been human rights violations on both sides, but that it was “particularly concerned” about evidence of torture and ill-treatment of civilians by Russian forces.
Russia is holding referendums in the regions – of Donetsk and Luhansk in the east and occupied parts of Kherson and Zaporizhzhia in the south – which have been strongly criticised by the West. It is expected Mr Putin will claim the poll of citizens, which has been carried out through a mixture of door-to-door visits from officials and voting at polling stations, will show overwhelming support for the areas becoming part of Russia.
Ukrainians living in the occupied regions have flooded the Russian-controlled checkpoints with the rest of Ukraine in a bid to escape before the areas are formally annexed. Reports have claimed some – even younger men – are being allowed through.
Russia announced a “partial mobilisation” last week of around 300,000 civilians, sparking protests and reports of queues at borders with countries such as Finland and Georgia as Russians move to escape the draft. On Monday, one conscripted soldier shot a military recruitment officer at a call-up centre in Ust-Ilimsk, Irkutsk.
Patriarch Kirill, the head of the Russian Orthodox Church and a close ally of Mr Putin, said Russian soldiers who died on the battlefield would have their sins absolved, adding that “sacrifice washes away all sins”.
The Russian-installed leader of an occupied region of Ukraine has said after annexation, Ukrainian “volunteers” living in the area will be sent to fight on the Russian side. Yevhen Balytskyi, head of the occupied parts of Zaporizhzhia Oblast, said locals would join the Russian army in its fight against Ukraine.
In a statement, the MoD said: "President Putin is scheduled to address both houses of the Russian parliament on Friday, September 30. There is a realistic possibility that Putin will use his address to formally announce the accession of the occupied regions of Ukraine to the Russian Federation.”
The statement added: “Russia’s leaders almost certainly hope that any accession announcement will be seen as a vindication of the ‘special military operation’ and will consolidate patriotic support for the conflict. This aspiration will likely be undermined by the increasing domestic awareness of Russia’s recent battlefield sets-backs and significant unease about the partial mobilisation announced last week.”
Meanwhile, the Russian Ministry of Defence has published a seven-minute video on its official Telegram channel that it says are interviews with Ukrainian citizens in Russia voting in Novy Oskol in the Belgorod region.
One quote, from a man named as Vladimir Buinak, allegedly says: “With the collapse of the Soviet Union, everything became very bad and, over time, our region, one might say, was destroyed. We are only for the Russian Federation, we are only for Russia. We were Russian-speaking, we studied in Russian schools.”
It is believed annexation could lead to claims from Mr Putin that its territory is under attack from Western weapons supplied to Ukraine.
On Tuesday, Dmitry Medvedev, deputy chairman of the security council of Russia, issued fresh threats to the West over the use of nuclear weapons in Ukraine.
He said: “Imagine that Russia is forced to use the most formidable weapon against the Ukrainian regime, which has committed a large-scale act of aggression, which is dangerous for the very existence of our state. I believe that Nato will not directly intervene in the conflict even in this situation.
"After all, the security of Washington, London and Brussels is much more important for the North Atlantic Alliance than the fate of Ukraine, which no one needs, even if it is abundantly supplied with various weapons.”
In February, shortly after the initial invasion of Ukraine, Mr Putin said he would recognise the regions of Luhansk and Donetsk as breakaway republics. The regions, which have had pro-Russian leaders installed since 2014, have been a location of conflict for the past eight years, with many Ukrainians opting to leave their homes there and live in other parts of the country.
In its report, the OHCHR said civilians were being badly treated in Russian-occupied areas of Ukraine.
The body said alleged violations of human rights included extrajudicial executions, torture and ill-treatment, sexual violence, ignoring fair trial guarantees, denial of medical assistance, lack of food and water, and poor sanitation.
It said: “OHCHR is particularly concerned about torture and ill-treatment of civilian detainees by Russian security forces and affiliated armed groups, which was documented in most areas under Russian control.
"Out of 38 civilians released from detention – 34 men, four women – and interviewed by OHCHR, 33 reported experiencing torture and ill-treatment while in detention. OHCHR also documented complaints about torture and ill-treatment in 34 cases of arbitrary detention and enforced disappearance perpetrated by law enforcement bodies of Ukraine.”