The partnership "is not directed against anyone, it`s not against Russia", she said.
But Russia cannot yet rejoin the G7 group of leading nations, she added.
"So long as Russia does not comply with basic common values, a return to the G8 format is not imaginable for us." The G7 - grouping top industrialised nations - meets in Elmau, southern Germany, next month.
Russia is exerting pressure on ex-Soviet states to join a Moscow-led "Eurasian Union".
A far-reaching EU-Ukraine association agreement angered Russia.
The Ukraine crisis erupted after the last Eastern Partnership summit, in Lithuania in November 2013. That was when former Ukrainian President Viktor Yanukovych - an ally of Russia - refused to sign the association agreement, in an abrupt reversal of policy.
He fled from Kiev in February 2014 amid vast anti-government protests in which more than 100 people died.
The pro-Western government, formed after fresh elections, signed the association agreement, but the crucial free trade part of it was suspended until January 2016 so that Russian concerns about it could be addressed.
"It`s not `either or` - partnership or not - so we are ready to talk about worries over the economic association with Ukraine," Mrs Merkel told the Bundestag - the lower house of the German parliament.
But she stressed that it was each partner state`s "sovereign decision if they want to forge close ties... nobody has a right to block that path".
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