Between 2011 and 2015, Lafarge paid 12.946 million euros to armed groups in order to keep its cement works in the north of the country open, according to a report commissioned when it merged with Swiss company Holcim in 2015.
Of this, more than 400,000 euros went to IS, which eventually took control of the factory in September 2014.
Former CEO Bruno Lafont has told judges that the first he heard of the payments at a board meeting in August 2014, a judicial source told the AFP news agency on Saturday.
"I did not comment at the time, except to say that the deal was not a good idea," Lafont said, adding that he then decided to close the plant.
"There are many things I did not know and that may have been hidden from me," he told the judges.
Deputy contradicts CEO
But Lafarge's Syria boss, Christian Herrault, said he kept Lafont regularly informed, according to the report.
"Mr Lafont never expressed doubts or any intention of closing the factory to Mr Herrault from that date and until August 2014," Herrault's lawyer Solange Doumic said.
The pair have been charged with "financing a terrorist organisation and "endangering the lives of others" along with Eric Olsen, who took over as CEO when the Holcim merger went through.
Three former officials at the factory were also charged in the case last week.