In an intelligence update, the organisation reports that Russia had assumed they would be met with limited resistance that would result in a rapid victory with minimal costs.
Many Western analysts had expected Mr Putin to use May Victory Parade to trumpet some kind of victory in Ukraine or announce an escalation, but he did neither. Instead, he sought to justify the war again as a necessary response to what he portrayed as a hostile Ukraine.
Posting the update, the MoD wrote: “Russia's underestimation of Ukrainian resistance and its 'best case scenario' planning have led to demonstrable operational failings, preventing President Putin from announcing significant military success in Ukraine at the 09 May Victory Day parade.
"Russia's invasion plan is highly likely to have been based on the mistaken assumption that it would encounter limited resistance and would be able to encircle and bypass population centres rapidly.
"This assumption led Russian forces to attempt to carry out the opening phase of the operation with a light, precise approach intended to achieve a rapid victory with minimal cost.”
It added: “This miscalculation led to unsustainable losses and a subsequent reduction in Russia's operational focus.”
Intense fighting remains in Ukraine with the conflict grinding through its 11th week.
The bodies of 44 civilians have been found in the rubble of a Izyum building destroyed by Russian forces in March, a Ukrainian official said.
Oleg Sinegubov, head of Kharkiv regional military administration said: "The bodies of 44 civilians were found in the temporarily occupied Izyum from under the rubble of a five-storey building, which was destroyed by the occupiers in the first decade of March,"
"This is another horrible war crime of the Russian military against the civilian population," he said on Telegram.
Izyum is an eastern Ukrainian city that Russia has been holding as a key frontline node.
It comes as Ukraine’s vital Black Sea port of Odesa is repeatedly bombed, including by hypersonic missiles.
The claims from the official have not been verified.