The amendments to clause 8 of the Bill, governing the reallocation of funds, would empower the Government to "by order provide for the money to be held for distribution by a different body specified in the order".
Mubeen Bhutta, policy officer at the NCVO, said: "It means the Government can decide who they are going to move money to. There's no one else involved in this process."
Tabled by lottery minister Richard Caborn, the amendments will be discussed at the standing committee, which meets twice this week.
However, they have already attracted fierce opposition from voluntary sector organisations.
"I'm nothing short of astonished at the audacity of the Government," said Kevin Curley, chief executive of the NACVS. "This fundamentally undermines trust between the voluntary and community sector and the Government."