Conservative MPs protested in the Commons last night that the government was intent on "bulldozing" through the Disqualification Bill, which would allow members of the Oireachtas to sit in the Stormont Assembly or at Westminster.
The Shadow Northern Ireland Secretary said the departure from the normal practice was "an abuse" of Commons procedures.
However, Mr Mackay admitted that the Conservative front-bench was "fairly agnostic about this Bill", while tabling an amendment seeking to make its implementation dependent on progress in meeting the decommissioning requirements of the Belfast Agreement.
Mr Mackay said that if IRA decommissioning had not begun by January 31st Mr Peter Mandelson "has absolutely no choice but to suspend the Executive".
There were fewer than 20 MPs, and only three from Northern Ireland, in the chamber as the Bill returned for its Committee Stage, having been approved at Second Reading on Monday night by 300 to 17 votes.
The Bill was due to complete its Commons stages last night before moving to the Lords.