Badia Arif Izzat, lawyer of former Iraqi intelligence director in northern Iraq, Farhan al-Jubouri, and Tariq Aziz, the former deputy prime minister, told Aljazeera.net that he would not attend the next session scheduled for October 30.
Saddam and six co-defendants are being tried for genocide against the Kurds during al-Anfal military campaign between 1987 and 1988.
Speaking to Aljazeera.net from Syria, Izzat said: "Around 1,000 documents have been stolen from my desk in the lawyers' lounge at the Iraqi supreme court building."
Izzat's office in Baghdad had already come under attack last month when armed men raided the office and kidnapped his secretary, stole computers and documents.
Izzat left Iraq last week, but he declined to say whether his departure was based on seeking personal safety.
Iraqi lawyers defending Saddam and his co-defendants are usually based in Jordan and go to Iraq only to attend court sessions. They usually fly to Baghdad and are transported under US army protection until they leave Baghdad again.
Last month, the US army refrained from providing protection to the defence team, causing resentment among them.
Three lawyers acting for Saddam's co-defendants have been killed since the series of Saddam trials started last year.