The committees, of course, have the power to summon witnesses, which they don't normally do. The departmental people and the ministers just turn up.
In relation to the bills themselves, the committees have no power to amend the bills. They can only make recommendations in relation to the bills. The Senate itself can amend the bills, reject the bills, but that is very infrequent.
There have been occasions when the Senate has declined to pass the bill until more information is provided. Amendments have been moved to bills to express difficulty with particular programs, but amendments are very rare. Mostly the appropriation bills go through unamended.
The whole purpose of this process is to refocus departments and the government on programs that might have difficulties. If you have something that's really controversial, that is really difficult, and there's a great deal of opposition to it, it may be the subject of an amendment or even a rejection, but that's very rare.