The businessman had complained that the officers sought Rs 2 crore from him so as not to name him in the case involving the 2008 Mumbai terror attack mastermind Saeed, the agency said on Tuesday.
The officers have been transferred out of the counter-terrorism agency unit until the matter was "thoroughly examined", the NIA said.
"A complaint of misconduct was received against the officers. An enquiry into the allegations is being conducted by a Deputy Inspector General-level officer. In the meantime, the three officials have been transferred out to ensure a fair probe," the NIA spokesperson said.
The NIA got the complaint about a month ago regarding the SP and two junior officers who were investigating the FIF.
"We have initiated an enquiry against the officials to maintain a zero tolerance policy against corruption. Strict action will be taken if they are found to have indulged in corruption," an NIA officer said.
The SP was earlier the chief investigation officer of the 2007 Samjhauta Express blast while the other two are from the intelligence and operations wings of the NIA, said the official, adding they had carried out searches against a businessman from North Delhi.
The names of the officials and the businessman are being withheld for now.
The NIA last year registered a case against the FIF's deputy chief Shahid Mahmood and others for hatching a conspiracy around 2012 to create sleeper cells and logistics bases in Delhi and Haryana under the garb of religious work.
After lodging the case, the NIA arrested Mohammad Salman and Mohammad Salim, both residents of Delhi, and later Mohammad Hussain Molani, a resident of Nagaur in Rajasthan.
In July, the NIA secured the deportation of Mohammad Arif Gulambashir Dharampuria, a trader from Valsad in Gujarat, from the United Arab Emirates.
The NIA has filed two chargesheets against the accused including Hafiz Saeed in connection with that case.
In the recent chargesheet filed on July 18, the agency named a 43-year-old person, Molani, for hatching a criminal conspiracy and under the Unlawful Activities (Prevention) Act.
According to NIA, Deputy chief of FIF Mahmood tasked his associate Mohammad Kamran, a Pakistani national based in Dubai, for re-routing funds from Pakistan to Dubai and further to India through hawala channels.
"During this preparatory work, the target persons were intended to be used for creating sleeper cells and hideouts," said the NIA, adding Kamran identified a few Indian nationals in Dubai and one person in India, Mohammad Salman, for this purpose.
( With inputs from IANS )