His comments come ahead of the final day of the committee stage of the Scotland Bill’s progress through the Commons where the devolution of Crown Estates is due to be discussed and agreed.
The Scottish Government has already complained about the number of potential vetoes on devolved powers held by UK ministers in the bill.
But Mr Fallon said the bill would allow the Ministry of Defence to protect its assets because the areas include the edges of Faslane on the Clyde where the Vanguard submarines which carry the UK’s Trident nuclear deterrent are based. The base is surrounded by Crown Estates seabed property and UK ministers fear the Scottish Government could use ownership to block submarines entering and exiting the base or, more likely, develop the areas in a way which would make Faslane unviable.
The Defence Secretary has made clear he wants the UK government to be able to prevent this from happening, particularly as the SNP has a record of using devolved powers to veto UK government policies with which they disagree.
In the past they have said they would use planning powers to veto new nuclear power stations being built north of the Border.
Mr Fallon is also concerned about training zones in places such as Cape Wrath in the north- west of Scotland which is Crown Estates property and where environmentalists have pushed for an end to UK sea battle trials because of the deaths of whales.
Another area of concern among many potential training areas in Scotland is the Firth of Forth.
The Defence Secretary, born and raised in Perth and Dundee, stressed he and the UK government respected the devolution process and were entirely supportive of Crown Estates land being devolved to Scotland.
He acknowledged the land, which includes many of the seabeds around Scotland and places like West Princes Street Gardens in Edinburgh and Kings Park in Stirling, could be used to make more money which could benefit communities across Scotland.
But he warned this could not be done at the expense of the defence of the UK.
The SNP has made its opposition to Trident clear, maintaining its position despite ending the party’s opposition to Scotland joining Nato should it become independent.
Both Alex Salmond, the SNP foreign affairs spokesman at Westminster, and defence spokesman Brendan O’Hara have made opposition to Trident a priority since the election.
The crunch moment is due to come next year when MPs are asked to vote on a “maingate decision” that will confirm whether Trident is replaced or not at a cost of £100 billion.
Mr Fallon said: “We cannot compromise the integrity of our defence, including the deterrent, by allowing the SNP to play political games.”
He added: “The only purpose of reserving this control over defence sites is to ensure that any future development is fully compatible with the way in which we operate our training and other defence activities in Scotland.”
He said there would be an agreement drawn up with the Scottish Government about any future developments so that the operation of MoD facilities would be safeguarded.
However, his words infuriated the SNP, which has accused Mr Fallon of being high-handed and disrespectful.
SNP Westminster leader Angus Robertson said: “Michael Fallon does his case no favours with this kind of language.
“It is clear the Tories have completely abandoned any idea of living up to the Smith Commission or recognising the mandate from the people of Scotland the SNP received in May, so to suggest we are the ones playing games is ridiculous.”
He added: “Trident is an obscenity – a total waste of money. Mr Fallon needs to stop being so high-handed and dismissive of people’s concerns.”