Parrikar said in the Legislative Assembly that inquiry would be conducted into sale of scrap worth Rs 14 crore by Arihant Shipping Company, which had won the tender to break up MV River Princess, the ship.
BJP MLA Michael Lobo, who raised the issue, demanded suspension of agreement signed by the government with it.
The company was yet to remove the shipwreck, he said.
Tourism Minister Dilip Parulekar said the tender was allotted during the tenure of previous Congress-led government.
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The company would not be paid till it clears away the entire wreck from the seabed, he said, adding "the tender is based on no cure, no pay basis. So if they fail to remove the entire ship, they won't be paid".
In a written reply in the House, Parulekar confirmed that a substantial portion of wreck was still on the seabed as per the 'magnetometer' and diving reports from National institute of Oceanography (NIO).
The ship ran aground at Candolim on the night of June 6, 2000. Last year, Arihant began the work to break it up.