After yet another attempt to redraw the organizational chart of their enforcement wing, top Environmental Protection Agency officials say they now are moving aggressively against those who violate the nation's anti-pollution laws.

"This organizational structure is working," according to Associate EPA Administrator Robert M. Perry. He said that in the past 2 1/2 months EPA has referred 31 cases to the Justice Department, compared with eight for the preceding six months.

But some EPA enforcement attorneys dispute top officials' claims that they are doing a better job of enforcing environmental laws than their predecessors.

"Absolutely ludicrous," said one. "The agency simply is not doing its job and cannot under prevailing conditions."

Another EPA enforcement attorney said that many of the cases cited by Perry were "not significant." He said some had already been "in the works" for several months or were "violations of consent decrees, which require little legal resources."

But Michael Brown, a top aide to Perry, said that the agency has not been engaging in "bean counting," or filing insignificant cases just to make the numbers look good.

Told that some career staffers at EPA still expressed concern over the agency's course, Perry seemed surprised. "I have been getting a positive reaction" from the enforcement attorneys, he said. "They tell me that they're very pleased."

In the year since Anne M. Gorsuch became EPA administrator, the enforcement office has been abolished, then reconstituted with a much smaller staff, then, most recently, cut from six to four divisions. Since March, Gorsuch has replaced her top enforcement officials, William A. Sullivan and Peter Broccoletti, shuffled the enforcement division chiefs and redefined the division's responsibilities and its relationships with the rest of EPA and the Justice Department.

When Perry took over in March as the top enforcement official, the agency was under fire from Congress for not pursuing enough cases. Congressmen, environmentalists and some EPA enforcement attorneys said the reorganizations and personnel shifts had, at least temporarily, crippled the enforcement effort.

Critics charged that if the Reagan administration couldn't rewrite environmental laws it would simply stop enforcing them. As evidence, they also cited attempts in May to demote nine of the 18 enforcement attorneys in Denver (at the GS12 level) to GS5 inspectors. After the lawyers' union filed suit, regional officials dropped the effort.

Perry said that, at the time, the attorneys were under the regional administrator's jurisdiction, not his. And he said charges that the Reagan EPA was trying to weaken the enforcement structure are "untrue."

But one enforcement attorney said continuity in cases "has been severely disrupted. Some cases have been bounced around three or four times in six months as a result of attorneys being moved from one division to another or responsibilities being shifted from one division to another."

And an internal EPA memo dated April 29 said, "There is considerable confusion in the regions now about who in HQ does what in the enforcement area and who to call to get something done."

Noting that now more headquarters people have to approve referrals of cases to Justice, the memo said, "Processing cases through HQ is much more elaborate than in the past. . . . Perception is that HQ doesn't really want the cases."

The internal memo, sent to Assistant Administrator Kathleen Bennett by Charles Elkins, one of her top assistants, said regional air-compliance staffers were confused by conflicting signals they said they were getting from top EPA officials.

Sullivan and Chief of Staff John Daniel had urged compliance staffers to be more aggressive, while Bennett had instructed them to defer more to the states, the memo said.

The memo said the regional staff was also concerned about the perception that the Reagan EPA will be more lenient on industry, causing some firms to think they "are in a new 'ball game.' This affects the speed with which negotiations can take place and the degree to which the industry undertakes voluntary monitoring which can serve as a means of EPA's detecting noncompliance."

EPA sources said they believe industry's attitude has also been influenced by the agency's decision to focus its efforts on major violators in heavily polluted areas of the country. An EPA enforcement attorney said such a policy "rewards the most recalcitrant polluters with a competitive advantage over companies which have complied with the law." He added that it also removes the incentive for small polluters or companies in clean air regions to meet air quality standards.

But Richard Wilson, director of the mobile source air pollution control office, said, "When you have limited resources it only makes sense to focus them where they will do the most good." He declared that EPA is "not encouraging small polluters."