A project agreement says the Dutch government will contribute Rs. 62.1 million and the Sri Lankan government will give Rs. 42.4 million.
Work was due to be completed by December 2012.
The then finance secretary P.B. Jayasundara and the Netherlands ambassador signed the cabinet-sanctioned agreement that was proposed by culture minister at the time Mahinda Yapa Abeywardena.
The project consultant was professor of archaeology at Sri Jayewardenepura University P.B. Mandawala, who has prepared the project estimates and reported progress of the work.
A recent inquiry found estimate reports had mentioned excessive prices, while the progress reports were all false.
For instance, documents said 20,328 cement bags had been bought, but only 7,700 bags had arrived at the work site.
Mandawala is accused of having his own ways in the project, and also that he had received salaries, allowances and other privileges by holding positions in other government projects at the same time.
Built by the Dutch in 1690, the Jaffna Fort is the second biggest of its kind in the country and suffered damage during the war.