Karen Bradley announced that the UK Government “intends to take steps to provide clarity” on a Stormont budget.
“This is clearly not where I want to be, but I have no other choice,” she said.
Ms Bradley made the admission in Parliament, on the first day it reconvened since talks to re-establish an executive in the devolved assembly broke down.
She said Northern Ireland “needs certainty and clarity” as it edged towards its 14th month without a government.
The Staffordshire Moorlands MP also revealed she was “looking at proposals” to pause or cap Assembly members’ salaries.
And she gave a firm rebuttal to claims from some leading Brexiteers – including one of her predecessors Owen Paterson – that the Good Friday Agreement had “run its course”.
“The people of Northern Ireland have come so far in 20 years,” she said.
“It is absolutely vital that we restored devolved government and we retain the Belfast Agreement.”
Ms Bradley added she would come back to Parliament to update MPs when she had more detail on a budget for Stormont.
She also praised James Brokenshire, who stepped down as Northern Ireland Secretary in January to focus on his health after discovering a lesion on his lung.
Ms Bradley called him an “outstanding” minister who was “very missed” and described in the “warmest, most generous terms”.
The Northern Ireland Secretary has been encouraged to impose a budget for the country by the Democratic Unionist Party (DUP), but urged not to by Sinn Fein.
DUP Westminster leader Nigel Dodds told Ms Bradley it was a “dereliction of duty” for her not to pass a budget.
“It’s time to get on with it,” he said.
It comes after power-sharing talks broke down between the DUP and Sinn Fein, with the unionists blaming differences over an Irish Language Act on there being “no prospect” of a deal.
Sinn Fein claimed that it was the DUP which “failed to close the deal”.