The chief coordinator of the prosecution's investigation arm Abdul Hannan Khan told the press that it had wrapped up the probe against the three.
He said the investigators heard testimonies of 65 witnesses.
"The probe report will be soon handed over to the prosecution of the International Crimes Tribunal," M Sanaul Haque, a senior member of the investigating body, told bdnews24.com.
In 2009, a case was filed against 12 people, including Siraj, accusing them of genocide, rape and arson during the 1971 Liberation War.
The case, filed by Nimai Chandra Das of Bagerhat's Raghuduttakatthi village, was later transferred to the tribunal.
On Jun 10, the International Crimes Tribunal-1 led by Justice Enayetur Rahim issued arrest warrants against the three.
Police arrested them between Jun 11 and July 20.