"The president ordered that your directorate be merged with the experts' directorate to carry out a pre-emptive strike against the bases of Khomeini guards," the memo read.
The term "Khomeini guards" refers to the Saddam regime's belief that Kurdish separatists were working with Ayatollah Khomeini, Iran's former supreme leader, during the Iran-Iraq war of 1980 to 1988.
Their bases were located "within the headquarters of the sabotaging 1st corps of Barzani" said the letter, referring to Mustafa Barzani, leader of the Kurdistan Democratic Party and now the elected president of Iraqi Kurdistan.
The general prosecutor also read from other documents in which prosecutors had highlighted the words "special ammunition" with yellow marker pens.
The defendants have insisted that the Anfal campaign was a legitimate operation against Kurdish separatists at a time when Iraq was at war with Iran.
Saddam has already been sentenced to death for his role in the execution of 148 Shias from the village of Dujail in revenge for an assassination attempt against him there in 1982.
Early this month, his lawyers appealed against the other trial's verdict and sentence. The appeal court is expected to rule in early January.