The House's $1.1 trillion spending bill has posed a problem for many Democrats, who want to pass legislation to keep the government running, but may also take issue with some of its stipulations. Among the attachments to the bill are a rollback of Dodd-Frank banking reforms and McCain-Feingold campaign finance regulation.
Still, battles over those issues would only be more challenging for Democrats when the GOP takes control of the Senate next year.
"If my colleagues don't like this deal, they're really going to hate the next two years," one congressional Democrat told NBC.
The White House indicated earlier that President Barack Obama would sign the bill, despite his disagreements with some of its language.
Pelosi sent her letter to colleagues after an expected 2 p.m. ET vote on the bill was delayed, raising suspicions that House Republicans did not have the votes to pass it.
Read MoreWhat does the spending bill do?
Dear Democratic Colleague,
It is clear from this recess on the floor that the Republicans don't have enough votes to pass the CRomnibus. This increases our leverage to get two offensive provisions of the bill removed: the bank bailout and big money for campaigns provision.
However you decide to vote in the end, I thank those who continue to give us leverage to improve the bill.