"INZ has no control regarding the number of people deported on completion of their prison sentence," Devoy said.
"INZ is prioritising the deportation of migrants who pose a criminal or other risk to public interest."
Those who provided false or misleading information in their visa applications and those who refused the agency's advice to depart the country voluntarily are also deported.
Deportation and removal cost the agency $1,996,118 and just $195,456 has so far been recovered.
The deportation level is expected to remain high after 54 illegal Malaysian workers were this week deported after a six-month investigation.
Operation Spectrum found the workers at construction sites, and were hired by third-tier subcontractors. It also found 15 who had previously been deported, but were able to come through the border with different names. Two even got permanent residency.
Another person arrested today on a charge of identity fraud has been bailed to appear in the Auckland District Court on Friday.
But Devoy said the "vast majority" of people deported are overstayers.
Last year, 566 or nearly seven in 10 of those deported had been in the country longer than their visa allowed them to.
Indian nationals topped the list of people deported on 232, followed by China on 85 and Tonga and Fiji with 73 each.
Devoy said the agency encouraged people to leave voluntarily and at their own cost.
Last year, 1437 people left voluntarily, up 83 from the previous year - also the highest since 2012-13.
"People who are deported are required to repay all costs before being granted any future visa to return to New Zealand," he said.
The New Zealand Association for Migration and Investment (NZAMI) however says the agency is to blame for the high number of temporary migrants becoming overstayers.
"We are finding that many applicants are finding themselves in an unlawful situation due to the processing practice by INZ," said association chair June Ranson.
Ranson said the length of time the agency takes to process visas and the interim visa did not give allowance for applicants to appeal when an application gets declined.
"If declined the applicant becomes unlawful, they cannot ask for a reconsideration as the migrant does not hold a valid visa," Ranson said.
"They then become liable for deportation."
People who enter New Zealand on temporary entry visas, such as visitor, student or work, become unlawful or overstayers after their visas expire or their applications for extensions are declined.
It is estimated there are about 11,000 overstayers currently in New Zealand.