More than two years after a fatal collision between two Tornado aircraft over the Moray Firth, Philip Dunne said a system was currently being tested on the planes.
But the more modern Typhoon jets do not currently have a planned solution, the minister said, warning about the significant challenges in designing a system for such powerful, high speed aircraft.
Speaking in a Commons adjournment debate called by SNP MP Angus Robertson, the Defence Equipment Minister insisted that training and other forms of risk management were crucial to ensuring safety, adding the RAF "is satisfied all risks to life associated with the operation of its fast jets are both tolerable and as low as practicably possible".
Mr Robertson has repeatedly called for collision warning systems to be installed on fast jets and the debate followed the publication last week of a service inquiry report into the Tornado crash and the Ministry of Defence's acceptance of liability for the incident in which three flight crew died.
Mr Dunne said: "The service inquiry did not conclude that the lack of a collision warning system caused the accident. The service inquiry specifically stated 'it is not possible to completely remove the risk of colliding with another aircraft regardless of the controls and mitigation put in place'.
"Therefore, a collision warning system is not a panacea - it cannot guarantee a mid-air collision would not happen again. What it does provide is an additional level of security and another tool for the air crew to use."
The minister outlined how most RAF fleets do have such a system and one for fast jets, which has "technological challenges", was currently being tested on two Tornado planes.
Mr Dunne said: "A third (Tornado) has been fitted for further development. On current planning, we intend to introduce this capability in stages from later this year.
"Analysis is currently under way into the potential to fit a collision warning system onto Typhoon aircraft but it is too early to provide a timetable for development of this capability... it is a very complex process and at this stage we are not far enough along in that process to be able to give clarity on either timetable or cost."
Mr Dunne said the F-35 Lightning II, due to be purchased to fly from the new Queen Elizabeth-class carriers in the next decade, will have a "limited" collision warning system built in.
The minister acknowledged the programme to fit collision warning system to Tornado was cancelled for three months in 2011 while the Ministry of Defence was working to balance its equipment budget. The decision was overturned by former defence secretary Liam Fox.
Opening the debate, Mr Robertson claimed a "series of negligent MoD decisions" may have led to the death of the pilots in his Moray constituency.
The SNP's Westminster leader and defence spokesman highlighted the fact a requirement for warning systems aboard Tornado GR4s was included in the 1998 Strategic Defence Review but the funding for it was not made non-discretionary and so it was then subject to delays.
He said: "The inquiry reports that the need for a collision warning system was highlighted 24 years ago within the Ministry of Defence following a collision in 1990.
"This start date is essential to understand what I believe follows and is an extremely serious charge - a series of negligent MoD decisions which may have led to the deaths of RAF personnel and the risk of many others.
"What was warned about has come to pass and three of my constituents died above the Moray Firth when their Tornados collided."
Mr Robertson said he wanted a full Fatal Accident Inquiry to be held, the equivalent of an inquest in Scotland, to allow witnesses to give evidence under oath.
Flight Lieutenant Hywel Poole, 28, Flight Lieutenant Adam Sanders, 27, and Squadron Leader Samuel Bailey, 36, died in the collision over the Moray Firth on July 3, 2012, while a fourth crewman was badly injured.
Air accident investigators said a collision warning system could have helped prevent the crash, in a report released on Monday.
The MoD said it will learn from the crash to prevent another similar incident.