Critics accused Rakhmonov, who came to power during the ex-Soviet country's civil war of the 1990s, of stifling dissent on Sunday.
They say recent steps - such as a referendum two years ago that gave Rakhmonov the right to stay in power until 2020 - threaten the country's stability and hopes for democracy.
Six parties are contesting 63 seats in Parliament's lower house, with 41 lawmakers to be chosen through direct voting.
The other 22 seats will be divided among parties that win at least 5% of the vote.
Rakhmonov's National Democratic Party is widely expected to keep its majority.
His only real challenger is the Islamic Renaissance Party, the core of the civil war opposition and now Parliament's only opposition party, with just two seats.
The other opposition parties have scant resources and few candidates.
At a polling station on Sunday, hospital worker Tatyana Saakian, 56, said she voted for an opposition party because she wanted democracy.
"Nobody can dictate what you must do," she said.
But another voter, teacher Rohat Abdusamadova, 46, said she supported the ruling party because "life has been steadily improving recently".
President Rakhmonov said he "voted for peace, national accord and Tajikistan's democratic development."
The president has given international observers assurances that the elections will be held in a democratic manner.
The National Democratic Party is
expected to keep its majority
Yet, in the past several months authorities have forced out of print several independent and opposition newspapers, and launched investigations of two opposition party leaders.
The Organization for Security and Cooperation in Europe has sent 130 observers to monitor Sunday's poll, in which 3.1 million people are eligible to vote.
Preliminary results are expected on Monday.
The pre-election period has been marred by opposition allegations that authorities were harassing their members, limiting their access to state media, arbitrarily detaining campaign activists and threatening to halt development projects or aid to areas that vote for the opposition.
Commenting on opposition and international observers' criticism of the elections, Rakhmonov warned that it was "dangerous to force democracy".
"One has to take into account every little people's mentality, culture, traditions and history - one has to remember that we are Asians," he said.
He also signalled on Sunday that he might seek another seven-year term in elections in 2006.
"I'm still young, energetic and not planning to leave politics," said Rakhmonov, who is 52.
The president rose to power during a five-year war between pro-government forces and what has been called a Muslim opposition which left 100,000 dead and devastated the Central Asian nation of 6 million people after the 1991 Soviet collapse.
A United Nations-negotiated agreement ended the war in 1997.
Rakhmonov has used public fears of a return to the bloodshed of the 1990s to keep his challengers in check, but the opposition warns that his heavy-handed rule will result in renewed violence.
"I'm still young, energetic and not planning to leave politics"
President of Tajikistan
A 31 January car bomb left one dead and three injured outside the Emergencies Ministry in Dushanbe.
No one claimed responsibility for the attack. Authorities claim it was a terrorist act, but gave no details.
Poverty is another problem, with an estimated 1 million forced to search for jobs in Russia or other former Soviet republics.