Merkel said she had noticed how difficult it had been for civil rights activists to be heard in Russia.
"I also regret that OSCE observers will not be able to take part in the elections there," Merkel told Deutschlandfunk public radio.
The Organization for the Security and Cooperation in Europe (OSCE), Europe's main elections watchdog, called off its observer mission for the election, citing a lack of cooperation, a charged that Moscow dismissed.
"We surely have a responsibility to again argue at length" to call for Russia's approval for free parties and for the respect of human rights, Merkel added. She hoped that Russia would choose to move towards being more open to different opinions.
Merkel acknowledged that under Vladimir Putin's presidency, Russians had more economic and material stability -- citing salary increases and paid pensions -- and that Russia played a more active role on the international stage.
"We depend on each other, but this does not mean we should not criticize on certain subjects that we view differently from the Russian president," she said.
Putin's certain to win
Putin's United Russia party is certain to win the election with a large majority. Eleven parties participated, but opinion polls predicted United Russia would secure at least two thirds of seats in the 450-seat State Duma, with the Communists a distant second, and other votes divided between Kremlin-friendly parties. For the first time since the 1991 Soviet collapse, pro-Western liberal candidates were forecast to be excluded from parliament.
Putin, 55, who is required by the constitution to step down next year after two Kremlin terms, heads United Russia's candidate list. He said victory on Sunday would give him a "moral" mandate in the future, fueling speculation that he intends to retain power.
"I'm sure that voters have determined their preferences and now only have to come and vote for the party whose platform seems convincing, vote for those people in whom you trust," he said after casting his ballot in Moscow, according to AP news service.
High voter turnout
Polling stations opened in a wave across the world's biggest country, from the Pacific Ocean to the Baltic sea. Turnout was brisk, the Central Election Commission said, despite voters having to brave icy temperatures.
"I voted for United Russia. Life's got better under Putin," Mohammed Egemberdiyev, a 43-year-old plumber, told AFP news service after casting his ballot at a polling station in central Moscow.
Opposition decries irregularities
The election followed a campaign marred by accusations that the Kremlin rigged the contest with controversial new election laws and media bias to ensure victory for Putin's party.
Observers from the Communist Party, seen as Russia's main opposition force, also reported "an enormous quantity of violations across the whole country," Andrey Klychkov, a legal expert for the party, told AFP.
Former chess champion and Kremlin critic Garry Kasparov, who spent five days behind bars last week for taking part in an unauthorized anti-Putin protest, called the elections a "farce" and said that Russian authorities were "raping the whole electoral system" with numerous irregularities.
"These elections are a reminder of Soviet elections when there was no choice," Kasparov said after casting his ballot, according to Reuters news service.
Exit poll results are expected after voting ends in Kaliningrad at 6 p.m. GMT.