"Neither party won more than two-thirds of the seats," he told reporters, estimating that no party received more than 70 seats, according to a tally by his supporters.
He also said that 200,000 of Phnom Penh's 722,000 voters had not been able to cast ballots because their names were missing from the electoral lists.
"We don't accept the result in Phnom Penh," Sam Rainsy, whose party held 24 seats in the last parliament, said. "I demand a re-run of the election in Phnom Penh to bring justice to voters."
"I call for a demonstration in Phnom Penh. I appeal to all people whose names were unfairly deleted - please hold a huge protest in Phnom Penh."
Election observers reported a number of cases of voters' names being removed from the lists, but they said they doubted the problem was as widespread as Sam Rainsy claimed.
"The atmosphere for the election day is better than past elections. But the most prominent point is that the turnout was low and a lot of names disappeared" Hang Puthea, head of the Nicfec group of election monitors, said.
"I can't believe that as many as 200,000 names went missing. I could believe the number is maybe 20,000."
About 17,000 domestic and international observers monitored the voting at more than 15,000 polling stations. More than eight million people were registered to vote.
Eleven parties were competing in Sunday's national poll, the fourth since the end of the civil war.
Voters in the capital Phnom Penh started lining up at dawn to cast ballots, with many saying their overriding concern was the territorial dispute with Thailand, centred on the ancient Preah Vihear temple.
|More than eight million people were registered to vote [AFP]
"I will vote for those who can solve the issue of Preah Vihear temple immediately after they take power," Lam Chanvanda, a 56-year-old businessman, said as he stood in a long queue of voters.
"Before I was never interested in the border, but now it is in my heart."
Thousands of soldiers from both sides are facing off near the 11th-century Khmer temple. Foreign ministers from the two nations are set to meet on Monday in hopes of resolving the deal.
Hun Sen has accused Thailand of ignoring international law and threatening regional peace by sending troops into the disputed zone around the temple.
"Everybody now supports the government because this is a national issue," Kek Galabru, a prominent Cambodian human rights activist and election monitor, said.
Hun Sen has ruled Cambodia since 1985, when he became prime minister of a Vietnamese-installed communist government after the Khmer Rouge were forced from power.
Previous polls held in Cambodia have been marred by violence. Scores of people - mainly opposition supporters and activists - were killed or beaten in the run-up to elections in 1998.
Election monitors say political violence has diminished greatly compared to past polls, but unequal access to the media is still a problem.