The additional cash is needed because the budget for protecting athletes and spectators has risen by more than three times the original figure.
Details of the planned new funding package emerged after the SNP administration and the new national police force requested more money in order to ensure a safe and secure event. The original budgeted amount was £27.2m.
The Scottish Government will have to find an extra £38m to cover the new total.
It follows last summer's debacle when troops had to be deployed at the London Olympics after private contractor G4S failed to recruit enough security staff.
In addition to almost £38m coming from the Government in 2014-15, the revised planned budget will be funded by raiding the Games contingency budget for just over £25m.
Opposition parties at Holyrood were briefed before the announcement on a shopping list of new measures and facilities requested by Police Scotland Chief Constable Stephen House in the wake of London 2012.
With millions watching the Glasgow event, just months before the independence referendum, the additional physical security systems include X-ray machines, lighting, fencing, barriers and both walk-through and handheld metal detectors.
There will also be further CCTV and PIDS (passive infrared detection systems) for the athletes' village and other venues, and also "hostile vehicle mitigation" – bollards and other devices to stop attackers driving at vulnerable points.
For security contractors, there is more money for competition venues and for other venues such as hotels. The measures will cover a longer period before, during and after the Games.
The police are being given additional funding for the main planning team, for policing Games venues and non-competition venues, including major hotels. There is also extra money for specialist cover of all the transport infrastructure, and for protection of VIPs (anyone moderately famous) and IPPs (internationally protected persons, such as heads of state).
The security budget had been increased as a result of key lessons learned from London 2012, which had a security budget of more than £1 billion.
Sports Minister Shona Robison told MSPs: "Scotland has an excellent track record of hosting and policing major events safely and securely – it's one of the reasons we won our bid to host the 2014 Games.
"The Scottish Government and Glasgow City Council, along with our partners, agree that we must not and will not take any chances with the safety of all those who wish to attend the Games. It is for that reason that we have accepted the advice from Chief Constable Stephen House that a safe and secure Games can be delivered for £90m."
The extra cash means that £461.7m of public money will be going towards the cost of the event, up from £424m, with £100m to be raised from commercial revenue, such as sponsorship and the sale of broadcasting rights, tickets and merchandise.
Ms Robison said security work for the Glasgow Games will be split into multiple contracts after the G4S row.
She said original planning had been for 50% of all security roles to be carried out by volunteers, but insisted: "When it comes to screening and
searching those entering venues, trained security personnel supported by the police are vital."
The minister also said security would be needed at the athletes' village from next month, not from June 2014 as had previously been thought.
There would also be cost implications for hotels and training venues that require a level of protection, Ms Robison added.
She told MSPs that as a result of the Olympics experience "we now know we need more CCTV, perimeter fencing and security checking equipment".
Ms Robison said: "This has substantial cost implications but is critical to ensuring that everyone is protected properly from the moment they are approaching the venue, right through to when they leave at the end of the day's events."
Labour's Patricia Ferguson said: "No-one wants to spend any more money on security than is absolutely necessary, but we do have to be prepared, and the safety and security of the athletes, visitors, volunteers and the spectators must be paramount.
"So I am pleased that the Scottish Government and its partners are facing up to this responsibility."
Ms Ferguson said it had "always been recognised that the budget for security would probably have to increase to reflect the best security advice as close as possible to the time".