Jenny Watson, the head of the Electoral Commission, also predicted "court battles" over the changes.
Her comments came as Labour leader Ed Miliband called on the Tory-Lib Dem Coalition to "think again" on the lobbying Bill, which he said would do nothing to clean up politics and would instead "gag" charities. The plans are designed to improve transparency in lobbying - which David Cameron has described as the next big scandal waiting to hit Westminster.
The proposals include the creation of a register of lobbyists, although those who work "in-house" for large firms would be exempt.
The rules would also cap at £390,000 the amount organisations, other than political parties, can spend at UK elections.
Charities and campaigners have also protested at plans to increase the number of organisations defined as campaigning ahead of general elections.
Appearing before MPs on the Commons Constitutional Reform Committee, Ms Watson warned the Bill's wide definition of "election purposes" gave her organisation a great deal of discretion to interpret what activity would be regulated as political campaigning "which we did not seek".
"It is likely that some of our readings of the law will be contentious and challenged, creating more uncertainty for those affected," she added.
Andrew Lansley, the leader of the Commons, told the same committee that charities should not fear the reforms, because they would not normally be campaigning for specific candidates or parties at elections.
He added: "Charities, pretty much by definition by virtue of charity law, should not be engaging in directly party political activity."
But Mr Lansley also acknowledged that the legislation would not prevent lobbying scandals.
These were already covered by existing laws, he said.