In addition to the direct indictments, the Public Prosecution Service of Canada announced new charges Wednesday against two of the men.
The moves breathed fresh life into the long-dormant terrorism cases that captured headlines two summers ago.
A hearing is scheduled for Thursday in Ontario Superior Court in Ottawa to set the latest proceedings in motion.
Misbahuddin Ahmed and Hiva Mohammad Alizadeh of Ottawa, and Khurram Syed Sher, of London, Ont., were arrested in August 2010 in the case known as Project Samossa.
They are all charged with conspiring to facilitate terrorist activity.
In addition, Alizadeh, 32, and Ahmed, 28, face counts of making or having explosives. And on Wednesday they were charged with participating in the activities of a terrorist group.
In 2010, police said they seized terrorist literature, videos and manuals, along with dozens of electronic circuit boards allegedly designed to detonate homemade bombs remotely.
Police said the purported plot reached to Iran, Afghanistan, Pakistan and Dubai. But no other details were made public.
The Public Prosecution Service handles proceedings involving offences under federal jurisdiction, working at arm's length from the attorney general. It has the authority to file direct indictments for a variety of reasons, including cases in which there has already been a substantial delay, or in matters where the safety or security of witnesses or their families may be at risk.
In keeping with prosecution service custom, spokesman Dan Brien declined to say why the cases will go directly to trial.
Alizadeh and Ahmed will face charges together, while Sher — at his request — will be tried separately. The two trials will take place in Ottawa, though with the exception of Thursday's hearing no additional dates have been set.
Sher and Ahmed are out on bail under strict conditions. Alizadeh remains in custody as he did not seek bail, and therefore must appear in court Thursday.
Matt Webber, lawyer for Alizadeh, said Wednesday he was surprised by the federal move to proceed directly to trial. Webber had been preparing for a preliminary hearing slated to begin next month.
Lawyer Mark Ertel, who represents Ahmed, was also puzzled.
"All it really does is deprive the accused men of the usual opportunity to test the Crown's case at a preliminary inquiry, which is a basic right that people charged with most indictable offences have," Ertel said.
"It seems odd to me and nobody's provided me with any explanation."
Ahmed worked as an X-ray technician at an Ottawa hospital, while Alizadeh had studied electrical engineering technology at Red River College in Winnipeg.
Sher, a doctor of pathology, once danced and sang on the Canadian Idol program.
Authorities said they made arrests when they did to prevent the suspects from sending money to counterparts to buy weapons that would be used against coalition forces in Afghanistan.