It means local government officials will have to produce a report within three days.
The intervention from Chief Justice Nasirul Mulk comes after the pair were beaten by a Muslim mob and then thrown into a brick kiln furnace after being accused of desecrating the Koran.
Their case has received condemnation from all quarters of the world and now legal authorities in Pakistan seem to be taking action.
Speaking about the development, Nasir Saeed from the Christian legal charity CLAAS-UK said: "We cannot avoid future such incidents unless the government takes stringent measures to stop the growing hatred and punish those who have been involved in such crimes.
"But unfortunately the government has always been hesitant to take action and bring those responsible for church attacks, the burning of Christian towns and villages, and the killing and burning of Christians alive, to justice.
"Therefore Christians have lost hope for justice from the present government, but after the suo motu notice by Chief Justice Nasirul Mulk, their hopes for justice for Shama, Shahzad and their unborn child have been raised."