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Mr Zelenskyy described as a "miscalculation" the decision led by France and Germany at the Nato summit in Bucharest that year not to admit his country to the alliance, despite a push from the US.
He was referring to the alleged atrocities against Ukrainian civilians by Russian troops, which world powers have described as "war crimes".
Mr Zelenskyy accused the European leaders of seeking to appease Russia with their stance that year.
But Mrs Merkel's spokeswoman said she "stands by her decisions in relation to the 2008 Nato summit in Bucharest".
"In view of the atrocities uncovered in Bucha and other places in Ukraine, all efforts by the government and the international community to stand by Ukraine's side and to bring an end to Russia's barbarism and war against Ukraine have the former chancellor's full support," the spokeswoman said.
Germany had considered it too early for Ukraine to join Nato because it found that the political conditions were not met at that point.
Mrs Merkel, who retired from politics late last year after four consecutive terms in power, had once been hailed as the leader of the free world.
But Russian President Vladimir Putin's war on Ukraine has exposed flaws in her legacy, with critics saying she left Germany and Europe vulnerable with her detente policy towards the Kremlin leader.
Under particular scrutiny is Germany's reliance on Russian energy, which made up 36 per cent of its gas imports in 2014 that rose to 55 per cent by the time of the February 24 invasion.
The dependence on Russian power has left Berlin saying it is unable to follow a call by the US and other allies to impose a full energy embargo on Moscow.
President Frank-Walter Steinmeier, who was foreign minister in two of Mrs Merkel's cabinets, on Monday admitted that he made a "mistake" in pushing for Nord Stream 2, the controversial pipeline built to double Russian gas imports to Germany.
"My adherence to Nord Stream 2 was clearly a mistake," Mr Steinmeier told German media.
"We were holding on to bridges that Russia no longer believed in and from which our partners had warned us about."
The US and EU members such as Poland had deeply opposed the €10 billion ($10.97bn) pipeline that bypasses Ukraine, depriving Kyiv of gas transit fees.
After obstinately defending it through its construction, Germany finally put the project on ice following Russia's invasion of Ukraine.
Mr Steinmeier has also come under fire over the pipeline project. His Social Democrats in particular have over the years pushed for closer ties with Russia.
Admitting his miscalculation, Mr Steinmeier said his "assessment was that Vladimir Putin would not accept the compete economic, political and moral ruin of his country for his imperial madness.
"Like others, I was wrong."