Janitors who clean many of New Haven’s largest office buildings may have mopped the floor with a new union contract announced Monday, but they still will make significantly less than Yale-employed custodians.

The Service Employees International Union Local 32BJ reached a four-year agreement this week with the owners of most of the city’s largest office buildings to organize local custodial workers, unionizing New Haven janitors for the first time. But while the deal boosts workers’ pay by more than 40 percent over the duration of the contract, their compensation still pales in comparison to wages guaranteed to University-employed custodial workers, who are represented by Local 35. Several of the office buildings covered by the contract house Yale administrative offices.

The agreement reached Monday includes about 300 janitors in New Haven, as well as about 200 others in office buildings scattered around the state. While the union’s organization efforts in Fairfield County five years ago met resistance from building owners and resulted in a janitor strike, Local 32BJ enjoyed widespread cooperation from New Haven building owners, union district chairman Kurt Westby said Tuesday.

“We talked to a lot of the owners before the campaign, and one of them asked, ‘Why did it take so long for you to come here?’” he said. “I think the owners were pretty sophisticated and understood the glaring differences between [janitors in] New Haven and the rest of the tri-state area — meaning minimum wage jobs and poverty.”

Local 32BJ, which represents about 90 percent of the contract janitors in Connecticut and also has a heavy presence in the rest of the tri-state area, began to ramp up efforts to organize New Haven-area janitors about a year ago. Under the terms of the agreement, full-time janitors’ pay will climb to a minimum of $10.50 an hour by the end of the contract, which also provides for health benefits for full-time workers.

Westby said that while the contract is a good first step, the many custodians who work on a part-time basis — and typically do not receive any benefits — still may face financial challenges. But the contract does guarantee more hours to workers by lengthening the minimum shift from four hours to five by the end of the contract, and that should help, he said.

“This contract moves the workers in a direction that they should be going,” Westby said. “We’re not done, but they clearly move by the end of the contract to have some dignity.”

The issue of unionization has also long been a controversy surrounding the new Yale Cancer Center, and in less than two weeks workers at Yale-New Haven Hospital will vote to decide whether to organize, a step nine years in the making.

While the union deal vaults local janitors’ total pay 42 percent over the course of the contract, custodial workers employed by Yale still fare significantly better.

Under the contract the University reached with Local 35 in 2003, Yale custodial workers currently earn a minimum hourly wage of $14.71, which will increase to $16.55 over the course of the next three years. A senior custodian now earns a minimum of $17.49 per hour, which will rise to $19.68 by the end of the contract.

Associate Vice President of Office of New Haven and State Affairs Michael Morand said Yale’s agreement with Local 35 provides custodial workers with wages and benefits, including full health insurance, far beyond what most institutions offer.

“Yale University is recognized as having the premier standard for wages and benefits for custodial staff in the state of Connecticut,” he said.

Though labor relations on campus are much improved since a bitter three-week strike during the 2003 contract negotiations, the University has faced a number of clashes with its unions in recent years. Last month, Locals 34 and 35 called for the University to increase pension benefits for 1,000 retirees who receive their pensions under an older union agreement.

Yale is not the only university to have faced accusations of short-changing workers. In 2001, Harvard University faced protests over its low pay for janitors. And as of 2000, 12 colleges and universities nationwide paid their custodians annual salaries below the federal poverty level, according to the Chronicle of Higher Education. In 2005, the national average hourly wage for an entry-level janitor was $9.98, according to the U.S. Department of Labor’s National Compensation Survey.

Mayor John DeStefano — whose failed 2006 gubernatorial bid was publicly backed by Local 32BJ — praised the union’s agreement as a boon to hard-working New Haven families.

“By standing together, these workers have made a powerful and simple statement: work should pay,” DeStefano said in a press release. “I commend them for their courage and commitment to improving the lives of their families and this community. We all want our children to have the chance to do better than we did — it is the definition of middle class — that’s what this contract is all about.”

The union contract covers about 10 million square feet of office space in the Elm City, including many of New Haven’s largest office buildings. Among the facilities covered are One Century Tower just beyond Timothy Dwight College at Church and Grove streets, the home to the Yale Office of Public Affairs; the Connecticut Financial Center at 157 Church St., which houses the Yale Office of Development; and the NewAlliance Bank building at 195 Church St.