The Cook Islands Democratic Party says the election count was inaccurate and it will challenge the result.
According to official results, the Cook Islands Party won an outright majority with 13 seats in the 24-member parliament.
The Democratic Party won eight but its leader Wilkie Rasmussen lost his seat to Willie John.
The One Cook Islands Movement has won two and one seat is tied.
The president of the Democratic Party, Sean Willis, says the vote count was mishandled.
"There are a lot of question marks hanging around about why a lot of Democratic votes by declaration were disallowed which were crucial in some outer island seats. There were postal votes that were accepted after the polling date. Basically we've lost the battle but we haven't lost the war. There are definitely going to be petitions."
Sean Willis says launching a petition costs about 5,000 US dollars and the party will have to decide in which electorates it can afford to challenge.