Four investigators are to arrive in Pakistan on Tuesday to question the students, including Rusman Gunawan, the brother of alleged top terrorist Hambali.
The students are among a group of 19 south-east Asians, captured this month in raids on Islamic schools in Karachi.
"We will discuss deportation when the team is here. We will respect Pakistani law," the Indonesian embassy's consular affairs chief, Dindin Wahyudin, told French news agency AFP.
No charges laid
The students are being held for alleged activities against Pakistani interests, but have not yet been charged.
Pakistani intelligence officials believe the 19 were a "sleeper cell" of the Jamaa al-Islamiya (JI) and are investigating whether they were planning attacks inside or beyond Pakistan.
They are also trying to establish how far their network extended inside the Islamic republic.
"Before these arrests we had no idea, because according to our data these students had no criminal background," he said, adding that there had been no prior request from Jakarta to arrest the six.
Pakistan has said the students will be deported once investigations are complete, but has not committed to any date.