The warning came almost two weeks after a Turkish teacher Kacmaz Mesut, his wife and two young daughters were deported, despite the court's stay order.
The family was picked up in September, allegedly blindfolded and bound before being loaded into trucks and taken away.
Some 285 Turkish nationals are also at risk and Islamabad must protect them "from forcible repatriation, arbitrary arrest," according to a statement by the International Federation for Human Rights.
"The government's deportation of a Turkish family should set off alarm bells," FIDH president Dimitris Christopoulos said in the the statement.
The father of the family was a former director of PakTurk International Schools and Colleges, private schools popular in Pakistan allegedly backed by US-based Turkish preacher Fethullah Gulen's Hizmet group.
Turkey to detain 121 ex-foreign ministry staff over Gulen links - media
Ankara accuses Gulen of masterminding a coup attempt against Erdogan's government in 2016 -- an allegation the cleric strongly denies -- and is seeking his extradition from the US.
The other 285 Turkish nationals are teachers associated with the PakTurk schools and their families, and they have been facing deportation to Turkey since November 2016.
They "live in fear of raids carried out by the Pakistani police and intelligence services," the statement said.
The rights activists said that Turkey has already succeeded in obtaining the forcible repatriation of teachers linked to the PakTurk schools from Malaysia, Myanmar, and Saudi Arabia.
"Pakistan flouted its international obligations simply to appease the Turkish government. It must reverse this approach with respect to the 285 Turkish nationals," Mehdi Hasan, chair of the Human rights Commission of Pakistan (HRCP) said.
Last November Pakistan deported dozens of Turkish teachers tied to PakTurk schools after a visit from Turkey's President Tayyip Erdogan, sparking small demonstrations in major cities.
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