The minister, who made a brief stopover at Hambantota on Wednesday, said there is an agreement that port remains free of military activities.
The port was leased to a Chinese company last year for operations for 99 years and there are concerns over its possible military use.
Sri Lankan government, has been maintaining that it will not permit China to use the port for military purposes.
Mr. Onedera, who arrived in Colombo after concluding his India visit, is the first Japanese defence minister ever to visit Sri Lanka.
His visit comes amid concerns over growing Chinese influence in Sri Lanka.
Pentagon in its annual report to the U.S. Congress last week raised concern about Hambantota terming it as a cautionary tale of China flexing its financial muscle via the Belt and Road initiative, creating dependence on chinese capital and paving the way for dominance in the Indian Ocean.