Work to redevelop the Sixfields Stadium stalled and the money, released in 2013, has yet to be recovered.
Police have been investigating "alleged financial irregularities".
Northampton Borough Council chief executive David Kennedy and borough solicitor Francis Fernandes have been questioned under caution.
The council has refused to comment because of the ongoing investigation. The BBC understands Mr Kennedy is currently on sick leave.
In a statement, a police spokesman said "no assumptions should be drawn" regarding interviews with "potential witnesses and suspects".
"Northamptonshire Police are independently collecting evidence and investigating a wide range of matters concerning the grant, use and loss of Northampton Borough Council public funds‎," he said.
"This search for the truth includes both making arrests and interviewing a wide range of individuals across many organisations."
The council's Labour leader, Danielle Stone, has called for full co-operation during the investigation.
"It's our money. We want our money back," she said.
"We can't really chase it if we don't know where it is. We won't know where it is until the police investigation has reported, so from my point of view the most important thing for the borough council to do is fully co-operate with the police and the auditors, so we get those answers and get them quickly."
On Monday it was revealed the council's bid to recoup the money using £950,000 of its own cash had been unsuccessful.
Two senior council officers have been questioned by police as part of an investigation into a £10m loan to Northampton Town Football Club.