The tripartite contract was signed between the IOA, the Meghalaya State Olympic Association and the state government here.
Meghalaya had made the bid to host the 39th National Games after successfully co-hosting the South Asian Games last year, they said.
State sports director Matsiewdor W Nongbri said the masterplan of the 39th National Games will be submitted by January 2019.
She said a working group, headed by Sports Minister Zenith Sangma, has been formed apart from a Land Bank Committee and Team Preparation Committee.
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Urban Affairs Minister R V Lyngdoh, congratulating the team behind the signing of the contract, said it was befitting to celebrate the state's 50th year by hosting the National Games.
IOA secretary general Rajiv Mehta said the signing of the host city contract will ensure that the Games go as planned and on time.
An estimated 14,450 athletes and officials are expected to visit the state during the Games, the officials said.