The changes would affect charity and other so-called 'society' lotteries, such as those benefiting sports clubs.
The Gambling Act 2005, due to come into force on 1 September, imposes annual fees of up to £6,361 on lotteries that raise more than £250,000 a year and accept stakes from players using remote channels, such as telephone calls or websites.
The fee is in addition to other charges for regulating lottery cash and cheque collections, and is payable to the Gambling Commission.
Hospices have been leading the campaign against the charge, which could affect as many as 75 hospice lotteries. Many derive only a small proportion of the sums they raise through remote giving.
"Most hospices have websites that collect lottery subscriptions, but they raise very little," said Garth Caswell, chair of the Hospice Lotteries Association. "They will now be captured by this legislation." The association has asked its members to lobby their MPs for an amendment to the rules.
A spokeswoman for the department said it was in discussions with the sector to address the problem, but added that society lotteries needed to be regulated.
"They have a lower regulatory risk than other lotteries, so they have been given a separate category of fees to reflect that," she said. "Small society lotteries that raise less than £250,000 won't need to buy a licence at all."
Midlands-based TLC Lottery has asked its players to join the campaign.
It raises more than £400,000 a year, which it splits between 128 good causes. "A charity lottery is not a commercial enterprise," said Colin Barrett, manager of TLC. "To pay would be tantamount to raiding the donation tin that supports our core beneficiaries."