"We have gone back to the other party (International Development Ireland (IDI)) to re-negotiate," permanent secretary Carter Morupisi said.
"We were re-directed by Cabinet to re-look at certain things," he added.
Speaking to Monitor at the launch of Air Botswana's new ATR 72-500 aircraft last week, Morupisi said the deal is still on, but there are "few issues that need to be discussed and clarified".
In his budget speech in February, Finance and Development Planning Minister Baledzi Gaolathe said government started fresh negotiations with IDI, which were successfully concluded. He announced then that the management contract would start by April.
"We had hoped that the negotiations would have been concluded by now," Morupisi said.
Even though the permanent secretary said he was not in a position to reveal the "certain things" Cabinet wanted revisited and the new deadline for negotiations to be concluded, he said he was optimistic the deal would be clinched "as quickly as possible".
Last year, Cabinet rejected a proposed management contract for the national carrier with South Africa's ComAir negotiated by the Public Enterprise Evaluation and Privatisation Agency (PEEPA). Government chose a management contract model after the initial privatisation proposed plan also failed.
On Thursday, AB took delivery of its first new ATR 72-500, in accordance with a deal for two ATR 72-500s signed last year worth US $ 37 million.
With its new ATR 72-500s, configured with 68-seats and equipped with the "Elegance Cabin" and In-Flight Entertainment, plus its refurbished fleet of 3 ATR 42-500s, AB will be introducing additional routes. The re-introduction of the route linking the country's two tourism top spots, Maun and Kasane, is among the priorities.
Other routes re-introduced are Kasane/Johannesburg and Francistown/Johannesburg.
This comes at a time when the competition is getting tougher after South African Airways (SAA) announced its entry into the Johannesburg-Gaborone route, whilst Kenyan Airways has also shown interest in re-entering the Botswana market.
Speaking at the launch, Works and Transport Minister Johnnie Swartz said government decided to re-fleet Air Botswana so that it rises to the challenging aviation environment and be able to respond to the needs of the passengers.
"When the second aircraft arrives at the end of May, Air Botswana will now be in a position to compete with others," Swartz said.
He also said the ongoing construction of the Sir Seretse Khama International Airport terminal and the extension of the runway was progressing according to plan. The expansion of the Francistown airport, he said, has already started.
For her part, AB chairperson Mpho Mothibatsela called on the airliner's staff to improve service delivery.
"Complaints such as late take-off, poor service delivery and luggage handling need to be addressed so that our airliner does not become an object of scorn."