For the first two years that New York City’s new lobbying restrictions were in existence, William Rapfogel had no idea he was violating them.

Figuring that the landmark 2006 law applied to big, professional lobbying firms, Rapfogel did not register anyone from the non-profit he heads, the Metropolitan Council on Jewish Poverty, as a lobbyist. After all, Rapfogel reasoned, his employees spent just a few hours lobbying lawmakers each year.

But after conversations with several attorney friends convinced him that he was wrong—any entity with over $2,000 in annual spending on lobbying must register their activities with the city clerk’s office—Rapfogel contacted the office for more information. He was immediately told to pay fines for the 73 days during 2008 that the organization had not been in compliance with the law. At $25 a day, the fine totaled $1,825. And since then, the organization has spent thousands of dollars in legal fees to stay in compliance with the highly prescriptive law.

Rapfogel’s advice to other non-profits is to learn from his mistakes “What I say to them is, ‘Talk with your lawyers and see what they tell you to do. But if you don’t file, nobody is going to bother you,’” Rapfogel said. “If you do file, be prepared for some harassment.”

A number of non-profit groups who deal with the current system say it creates disincentive to follow the law: small nonprofit organizations are almost never fined for failing to register as lobbyists, but when they do register, they are often fined heavily for everything from late filings to arcane paperwork mistakes.

According to a March 2009 report released by the clerk’s office, during the first two years under the new lobbying law, not a single fine was levied for a failure to register as a lobbyist. At the same time, in 2007, lobbyists and their clients were fined $330,075 for filing late reports, and in 2008 they were fined $232,025.

The report also shows that even as awareness of the city’s lobbying laws has become more widely disseminated, the number of lobbyists who have registered with the clerk’s office has actually decreased. In 2007, 378 lobbyists were registered, according to their report. In 2008, only 364 were registered.

Allison Sesso, a lawyer who is the deputy executive director of the Human Services Council of New York City, works with non-profits to help them comply with the city’s lobbying laws. Though Sesso encourages these non-profits and their employees to register, she says the current law does the opposite.

“It’s basically encouraging people to break the law,” Sesso said.

The 2009 report does mention six cases of unreported lobbying that were disclosed to the clerk’s office by the public, and the report states that thes cases are under investigation. The results of these investigations may become public when the clerk’s 2010 report is submitted March 1.

The city clerk’s office declined comment for this article.

Sesso said one problem is that the lobbying division of the office does not have the resources to monitor whether the city’s thousands of non profit organizations are meeting the $2,000 lobbying threshold. Sesso said she believes the solution would be to raise the minimum threshold at which entities are required to register lobbying activities—the state’s lobbying laws have a $5,000 threshold, for instance—in order to relieve the burden on the clerk’s office and allow their limited staff to focus on the bigger, professional lobbying firms.

Rapfogel, meanwhile, suggested that to alleviate the amount of work for the city clerk’s office, smaller non-profits could simply register with the state only, rather than with both the city and the state.

Non-profit organizations concerned about this issue have been in talks with Council Speaker Christine Quinn’s office. A revision of the city’s lobbying law could potentially be on the agenda this year, they say.

Rapfogel, for one, is hopeful that a change in the city’s lobbying laws will be forthcoming.

“The purpose of this law was really to focus on the big lobbyists that are powerful enough to defend themselves,” Rapfogel said. “Instead, they ended up beating up on the non-profits.”