Sunday's election was the first since Kosovo unilaterally declared independence from Serbia in 2008 and observers and the opposition have raised questions about a high turnout in Thaci strongholds.
"Democracy is being violated on a large scale in Kosovo and the legitimacy of these elections is now in question," Democratic League of Kosovo (LDK) leader Isa Mustafa told reporters.
"We have submitted our complaint to the competent authorities and will await their decision," Mustafa said.
Preliminary results based on a count of almost all of the votes give Thaci's Democratic Party of Kosovo (PDK) 33.5 per cent, with the LDK trailing with 23.6 per cent. The final results are due by the end of the week.
Mustafa said his party's main complaint was a suspiciously high turnout in Thaci's stronghold region of Drenica where local elections authorities reported more than 90 per cent of people had cast their ballots.
European parliamentarians, international watchdogs and even US ambassador to Kosovo, Christopher Dell, have also commented on the Drenica situation.
Mustafa said the LDK's legal challenge, submitted to a special court panel, also included other irregularities spotted by his party. Further steps would depend on the court's ruling, he said.
"The LDK will not allow Kosovo to be governed with a manipulated vote because one who manipulates the vote will manipulate rights of the citizens, the resources of Kosovo and the future of this country," Mustafa said.