Guinea's exiled former junta leader Moussa Dadis Camara has told the BBC Guinean authorities are blocking him from returning home.
His attempt to return via Ivory Coast this week failed when his flight was refused permission to land in Abidjan.
On Thursday, President Conde denied involvement, saying Ivory Coast was a sovereign country.
Capt Camara says he wants to stand for president in October's elections and the deadline to register is on Tuesday.
He has been living in Burkina Faso since an assassination attempt in December 2009.
"I think President Alpha Conde does not want me to come back home," Capt Camara told BBC Afrique.
"The instructions [for the plane not to land] came from Conakry not Ivory Coast."
Capt Camara, who seized power in 2008 when long-time leader Lansana Conte died, announced his attention in May to stand as the presidential candidate for his Patriotic Front for Democracy and Development (FPDD) party.
Two months later, Guinean judges indicted him for his role in a 2009 massacre in the capital, Conakry, in which more than 150 people protesting against the military rule were killed.
'Will face justice'
He told the BBC he was prepared to turn himself over to the courts in order to prove his innocence.
"I have never refused to face justice," he said.
Little-known outside military circles before he seized power in December 2008, Capt Camara is popular in the south-east of the country, near the border with Liberia and Ivory Coast.
He has also signed a political alliance with opposition leader Cellou Dalein Diallo, who will be running for president.
Capt Camara said it was not the first time he had been refused permission to return.
In April 2013 he had asked to attend his mother's funeral, but he said official channels turned him down so he entered the country unofficially via Liberia to get to his village.
Explaining about his failed attempt on Wednesday, he said the captain of the commercial flight had been diverted to Ghana.
"When we disembarked, the captain confirmed that he was told that I should not land at Abidjan, where I had a connection to join Guinea," said Capt Camara, who is now back in the Burkinabe capital, Ouagadougou.
President Conde, who won elections in 2010, Guinea's first democratic vote since gaining independence from France in 1958, is running again in October.