A former presidential bodyguard and an opposition politician have alleged that Ukrainian President Leonid Kuchma ordered the journalist's assassination, and there have been mass demonstrations calling for his resignation.
Mikhailo Potebenko said experts were 99.66% certain of the identification, following DNA tests, but he called for further analysis.
A former presidential bodyguard and an opposition politician have alleged that Ukrainian President Leonid Kuchma ordered the journalist's assassination, and there have been mass demonstrations calling for his resignation.
Mr Kuchma has denied the allegations, and the authorities have staged counter-demonstrations in his support.
Mr Gongadze, aged 31, was the editor of an online newspaper, Ukrainska Pravda, that had been outspokenly critical of Mr Kuchma.
He disappeared in September.
US concern
The body was discovered on the outskirts of the village of Tarashcha, north of Kiev, two months later.
A local coroner's report on the body, which apparently identifies it as Mr Gongadze's, was never officially released.
The allegations of Mr Kuchma's involvement in the case rest on audio tapes, in which a voice is heard urging that Mr Gongadze should be "abducted by Chechens".
Mr Potebenko told parliament that it was impossible to determine whether the tapes were genuine, because they contained "editing, removals or inserts of separate fragments, words and sounds, and were of low quality".
The former bodyguard who released the tapes, Mykola Melnichenko, has been charged with slander and forgery.
On Tuesday a Ukrainian parliamentary commission investigating Mr Gongadze's disappearance accused prosecutors of eliminating evidence linked to the case.
The same day, the US State Department said any friend of Ukraine had to follow the Gongadze affair "with concern", and called for a "speedy and transparent" investigation.