Federal prosecutors say the men had tried to buy uranium
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Two men suspected of trying to buy uranium for a suicide attack were due to go before a German judge on Monday.
Al-Qaeda suspects Ibrahim Mohammed K, 29, and Yasser Abu S, 31, were detained during early morning police raids in Mainz and Bonn on Sunday.
The judge is due to rule whether there is enough evidence to hold the men.
Chief Federal Prosecutor Kay Nehm said the men had been under police surveillance though it is not known where their alleged attack was planned.
The BBC's Ray Furlong in Berlin says the arrests come at a sensitive time, as US President George W Bush is due to visit Mainz next month.
Nationwide raids
Germany has been trying to clamp down on Islamist groups since it emerged that some of the 9/11 hijackers had a base in Hamburg, our correspondent says.
Ibrahim Mohamed K, an Iraqi, is accused of having links with Ramzi Binalshibh, thought to have been a key member of the Hamburg cell.
He also allegedly trained at al-Qaeda camps in Afghanistan and had links with Osama Bin Laden.
Earlier this month, German police detained more than 20 suspected Islamist militants in raids across the country.
In December, they arrested three men they claimed were planning to attack the visiting Iraqi Prime Minister, Iyad Allawi.