Moort Boodjari Mia in Perth received an 11th-hour offer from St.John of God Health Care to run a 12-month trial integrating the clinic into the new Midland hospital.
The clinic, which has won two national health industry awards since it opened in 2011, provides maternity care to indigenous teenagers and women.
Focussing on at-risk women, it has seen a 70 per cent increase in attendance at appointments since its inception.
That has meant more women are less likely to engage in dangerous behaviour like smoking, drinking or taking drugs while pregnant.
Despite its success, the State and Federal Government cut its funding to the service because they could not agree who should support the program.
The decision to close the centre angered the community and a petition calling on the WA Health Minister to fund the scheme secured more than 20,000 signatures.