The extent of the rock at the entrance was underestimated during initial surveys and the extra requirement for expensive underwater blasting and dredging raised the basin excavation and channel dredging costs by almost half.
Sri Lanka Ports Authority chairman Priyath Wickrama said the rock had now been cleared.
"Today no one is talking of the rock that was supposed to be blocking the entrance channel," Wickrama told a meeting of the import section of the Ceylon Chamber of Commerce.
"We have completed the dredging work. Now there is no rock at all."Hambantota port is being built by a consortium consisting of China Harbour Engineering Corporation and Sinohydro Corporation and funded with Chinese government loans at commercial lending rates.
The government came under heavy criticism for the late discovery of the rock and the additional cost of clearing it.
Wickrama also said investors who planned to put up industries and service businesses in Hambantota would begin building factories in December.
A request for proposals in 2010 had drawn 27 proposals of which 14 were shortlisted and an initial four had been approved by the Cabinet of ministers.
"We have got Cabinet approval for four investors who will invest 700 million US dollars," Wickrama said. "In December they will start construction of factories. "They have guaranteed us cargo volumes and will pay us a guaranteed royalty."