Self-declared National Resistance Movement "general" Miguna Miguna was illegally issued with a Kenyan passport in 2009, the government has said.
Interior spokesman Mwenda Njoka said the passport, though issued by the Immigration ministry, was illegal because "without following the requisite legal process, then Minister for Immigration, the late Otieno Kajwang' ordered that Miguna be issued with a Kenyan passport."
In a statement, he added: "At the time he was working as an advisor to then then Prime Minister Raila Odinga. Prior to being illegally issued with a Kenyan passport, Miguna had been travelling using Canadian Passport No. MJ 393885 and WK 944502. Miguna renewed his Canadian passport in June 2017 just a few weeks to the general elections."
And since it was before the promulgation of the new Constitution, Mr Miguna was required to denounce his Kenyan citizenship.
The 2010 constitution allowed for dual citizenship.
"When Miguna acquired Kenyan passport in March 2009, he deliberately failed to disclose the fact that he had acquired citizenship of another country and therefore the Kenyan passport he acquired then was and still remains illegal," Mr Njoka also said.
Application for the disputed passport was at Kisumu Passport Control.
Mr Njoka went on: "The late Minister's orders that Miguna be issued with a Kenyan passport without following the proper legal procedure as prescribed by law was illegal and had no backing in law.
The political activist deported back to Canada on February 6.
Mr Njoka said the deportation is supported by law.
He added: "Based on the provisions of section 33(1) and 43(1) of the Kenya Citizenship and Immigration Act, 2011."
The spokesman went on to give a history of Mr Miguna run in with the government.
"Miguna fled Kenya in 1988 using travel documents provided by a foreign country. Thereafter he acquired Canadian citizenship and has remained a Canadian citizen since then. Miguna acquired Kenyan passport in 2009 at a time when it was illegal for a Kenyan to hold dual-citizenship without having denounced the foreign citizenship.
"Prior to this, Miguna had applied for Kenyan Passport in 1987 to enable him travel to Cuba for a students' conference. His application for passport was rejected in a letter dated September 12,1987 which gave Miguna reasons for the rejection. At the time Miguna was a students' leader at the University of Nairobi before he was expelled from the University," the statement read.
When the new Constitution came into force, Kenyans who had lost their citizenship as a result of acquiring other nationalities were required to officially apply to regain their Kenyan citizenship.
"Miguna never did this and therefore continued being a Canadian citizen," the statement also said.