Scott had been selected in the Scotland A squad to compete in the Churchill Cup in Canada but he has been forced to withdraw.
Scott, from St Helens, joined Glasgow in 2004, and qualified on residency grounds last August. At the end of the season he signed for Leeds Carnegie in the English National Division One but did not expect that to affect his plans to play for Scotland A. However, his hopes of international honours have been dashed because he has sold his house in Glasgow.
Scott told The Scotsman: "I sold my house to teammate Bernardo Stortoni in May and arranged to move in with Graeme Morrison temporarily while I prepared for the Churchill Cup. I was stunned and really gutted when I got a call to say the IRB had refused to clear me on the grounds that on the date of the first game in June I will only have a rented address in Scotland."
If Scott played for Scotland A at any time during this season he would have been clear to continue no matter where he lived. An SRU spokesman explained: "Until recently Scott owned a home in Glasgow and could claim primary and permanent residence. Not fully aware of the stringent IRB rulings surrounding qualification through residency, he sold his home in preparation for his move, and moved into temporary rented accommodation. Unfortunately, Scott is no longer eligible for Scotland as he no longer has his primary permanent residence in Scotland."
Scott added: "If I'd known about this ruling I wouldn't have sold Bernie my home until after I'd toured. But it's not to be. My hopes of playing for Scotland are dead and buried now."