No Americans were killed or wounded in the embassy attack, American military officers said.
He was told to plan the embassy attack for the end of the year or early next year.
Four Qaeda members were convicted in 2001 for the embassy attacks.
It was the third embassy attack by the Guatemalan terrorist group in the last six months.
But the interceptions could not prevent the embassy attacks.
But the new charges are an indication of how quickly the Government has worked to solve the embassy attacks, which occurred just three months ago.
They've lost hundreds of their citizens in this embassy attack.
The battle did not appear to be directly related to the embassy attack.
The ruling came two days before the first anniversary of the embassy attacks, which killed 223 people and wounded more than 4,000.
That, the government says, led to the 1998 embassy attacks.