Chad said some of the prisoners were Sudanese
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Chad's government says it will continue house-to-house searches to seek rebels in the capital, N'Djamena, following a coup attempt earlier this month.
A BBC correspondent says the raids have terrorised parts of N'Djamena.
Interior Minister Mahamat Ahmat Bachir was speaking after dozens of alleged rebels, many of them children, were paraded in front of journalists.
He also said an enquiry had begun into the whereabouts of three missing opposition leaders.
Meanwhile, France has acknowledged that its forces transported weapons to Chad's army as it beat back the rebel assault on N'Djamena.
A French spokesman said the weapons were flown in from Libya and other countries.
He said former colonial power France had acted in accordance with a military co-operation agreement between the two countries.
Dishevelled
Mr Bachir said those alleged rebels who were under 18 would not get special treatment, calling them "child mercenaries", not child soldiers.
He said the house-to-house raids would continue until all the rebels had been found.
"Anyone who hides a rebel will be treated as a rebel."
The BBC's Stephanie Hancock in N'Djamena says many refugees who have fled Chad say they are too scared to return home.
She says some fear that a government crackdown on those accused of supporting or sympathising with the rebels is getting out of hand.
Those alleged rebels already caught were forced to sit in rows as journalists were invited to film and photograph them in a compound in the capital's police headquarters.
Our correspondent says they looked dishevelled and exhausted and many were painfully thin.
In a separate room injured prisoners lay on a bare, concrete floor. Many had intravenous drips inserted, hanging from a string on the ceiling.
Mr Bachir said many of them were Sudanese - Khartoum has denied Chad's accusations that it backs the rebels.
'Kidnapped'
On Wednesday, France and human rights group Amnesty International expressed their concern over the fate of the missing opposition leaders.
The three, who include former President Lol Mahamat Choua, disappeared while rebels were attacking the city.
The opposition say they were seized by government soldiers but the government says they went missing from parts of the city controlled by the rebels.
The other two are opposition alliance spokesman Ibni Oumar Mahamat Saleh and veteran Ngarlejy Yorongar.
"They were kidnapped by about 15 soldiers from the presidential guard," a spokesman for Mr Choua's Assembly for Democracy and Progress said, reports the AFP news agency.
A European Union peacekeeping force is due to arrive in Chad this month to protect refugees who have fled the Darfur region of neighbouring Sudan.
Their deployment of the 4,000-strong force was delayed by the rebel attacks.
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