Benny Wenda, the leader of the United Liberation Movement of West Papua, arrived in Port Moresby from the United Kingdom on Tuesday.
He was detained upon arrival at Port Moresby's International Airport and told by immigration officials he was banned from entering the country.
It is believed national capital district governor Powes Pakop invited Mr Wenda to visit PNG to rally support from the government for the inclusion of West Papua into the Melanesian Spearhead Group.
His deportation was delayed when prime minister Peter O'Neil intervened, saying he was not aware of such a ban.
It was not known who issued the order to ban Mr Wenda from entering the country.
The prime minister said he met with Mr Wenda, along with Mr Parkop and PNG immigration officials, to discuss the issue.
Mr Wenda remained at the airport on Wednesday awaiting clearance to enter the country. [ABC]