Colleagues had been trying to contact John Bosco Gasasira, editor of the opposition website Umuvugizi since mid-January, and he only appeared after the expulsion of a foreign diplomat from Sweden, believed to be a Rwandan.
"I could not keep my phones on. I knew Rwandan agents were hunting me," Gasasira told the media rights group.
"Gasasira alleges that Rwandan agents in Sweden have been monitoring him since September 2010 and even attempted to poison him," the CPJ added.
The Swedish government said Tuesday it had expelled a foreign diplomat, but would not confirm reports the person was a high level official at the Rwandan embassy in Stockholm.
Opposition reports said Rwandan diplomat Evodo Mudaheranwa was last week given 48 hours to leave Stockholm for "activities incompatible with his diplomatic status."
"Evode Mudaheranwa was evicted the same day I came out of hiding," Gasasira told the CPJ.
Gasasira was sentenced in absentia last year by Rwanda's supreme court to two years and six months in prison on charges including insulting the president.
He left Rwanda in August 2010 after his newspaper was suspended, switching instead to running his website abroad.
Meanwhile, Rwanda's supreme court said Friday it would issue its verdict on March 16th in the appeal of journalists Agnes Uwimana Nkusi and Saidati Mukakibibi, who are serving jail terms of 17 and seven years respectively.
Nkusi, editor of the Umurabyo monthly, was last year convicted of defamation, causing divisions and denying Rwanda's 1994 genocide. Mukakibibi, the publication's reporter, was found guilty of inciting civil disobedience.
The case is being watched closely by human rights observers and could potentially have far-reaching implications for media freedom in Rwanda.