The criticism came as ministers met charity groups concerned about the plans, due to be debated by MPs today.
Prime Minister David Cameron has warned that lobbying is the next big "scandal" waiting to hit Westminster.
His government wants to create a statutory register of lobbyists and limit to £390,000 the amount organisations - excluding political parties - can spend at UK elections.
But ministers have been accused of a botched job that will hit the charitable sector.
Critics say so-called "in-house lobbyists" will be exempt from the register.
The proposals will raise the number of third parties required to register with the Electoral Commission, the UK's elections watchdog.
Michael Clancy, director of law reform at the Law Society of Scotland, said the proposals could "stifle legitimate public debate".
"We are concerned that by increasing the administrative burden the bill could deter third party organisations, such as charities and non-political organisations, from actively engaging in public policy discussion, even where this is for non-political purposes," he said.
Margaret Curran, Labour's shadow Scottish Secretary, said the bill would put a "heavy burden on Scottish charities, and restrict the work they do to improve the lives and livelihoods of people across Scotland".
She added: "If passed, it would amount to a gag on charities and campaigners who want to criticise and scrutinise the work of the UK Government."
But Downing Street rejected warnings that charities would be prevented from speaking out.
The Prime Minister's official spokesman said that only a small number of charities which explicitly promote parties or candidates would be affected.
Oxfam, the Royal British Legion, and the Salvation Army among those that have expressed fears over the Bill, which campaigners warn is complex and unclear.