The charges come amid signs of increasing militancy in the East African nation. Ethiopian troops moved into Somalia at the beginning of the year to fight the Somali militant group al-Shabab.
Prosecutors said the suspects, who include one Kenyan national, formed a cell with the al-Qaida-linked group.
Five suspects are in custody. Six others are to be tried in absentia.
The charge sheet says the suspects have been mobilizing resources to train recruits and carry out attacks aimed at destroying Ethiopia’s political, economic and public establishments.
On Tuesday, the five suspects challenged the charges and asked the court the throw out the case. The court on Thursday rejected the request.
Prime Minister Meles Zenawi in April told parliament that militants had formed al-Qaida cells in the country’s southern Arsi and Bale areas.
Ethiopia’s military push against militants in Somalia from 2006-2009 angered al-Shabab and led to intensification of the insurgency.
There are signs of rising militancy in Ethiopia. In late April a clash, triggered after security forces arrested a Muslim religious leader in the Oromia region, left four demonstrators dead.
The country’s Federal Ministry on May 3 issued a statement accusing an unnamed group of trying to declare jihad against the government and incite violence in a number of mosques across the country. The statement said a dozen suspects were recruited by the group from the country’s Oromia, Tigray and Amhara regions to carry out illegal activities.
The government also expelled two Arabs who flew in from the Middle East on May 4. The government said the pair went to a mosque and tried to incite violence.