Arseniy Yatsenyuk said the Ukrainian people wanted a "European perspective" for the strife-torn former Soviet republic, which is facing an armed secessionist movement in parts of the east.
Pro-Russian militants have seized control of government buildings and clashes have left scores dead.
"The Berlin Wall has fallen and there will never be a new Berlin Wall in Europe," Yatsenyuk said in a statement, standing alongside Merkel and his counterparts from Georgia and Moldova in Berlin.
"The Ukrainian people expect change from us."
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And he called for all countries, including UN Security Council members, to recognise Ukraine's elections and its "legitimately elected president".
For her part, Merkel voiced concern about observers from the European security body OSCE who are missing in Ukraine.
"We are at the moment of course worried about the OSCE observers but we will do everything to get these observers free," she said.