Missions Interlink was established in 1986 at a national forum of evangelical missions in Canberra. It was considered expedient, conformable to the will of God, expressive of discipleship to the Lord Jesus Christ, and a step towards facilitating fulfilment of His great Commission, to constitute an Australian Commission of evangelical missions.

However, state missions commissions had existed in most states for many years, and until 2005 continued to maintain their own identities and separate memberships, and were regarded as member agencies of the national body in their own right.

In 2005 Missions Interlink membership was nationalised and the state missions commissions became Missions Interlink Networks of the national body, and continue to be responsible for Missions Interlink activities at the state level. the national office of Missions Interlink continued to provide information, services, and advocacy to its members, with an additional focus on encouraging ministries and networks to function at a national level.