WASHINGTON - House Speaker Thomas P. "Tip" O'Neill Jr., in a rare appearance as a congressional witness, praised President Reagan's tax reform plan as a "historic shift" for the White House and said a bill could pass by the end of next year.

But, testifying Thursday before a House Ways and Means subcommittee, the Massachusetts Democrat stressed that while the proposal was a good beginning, one of his "very highest personal priorities" will be to make tax reform more attractive to the working poor.

Even if the Reagan plan is enacted, he said, "The working poor will still be paying more taxes than they did before he took office."

"Reducing the tax burden on the working poor is the very heart and soul of tax reform," O'Neill said, calling the current tax system "an obstacle course for hard-working people who are struggling to raise themselves and their children out of poverty."

"By any reasonable standard of social policy, tax laws should encourage poor people to work instead of taxing them at such high rates that they must wonder whether they would be better off on welfare," O'Neill said.

He attacked Reagan's 1981 tax bill that gave large breaks to corporations and the wealthy and noted, "The president's proposed tax reform bill moves in the direction of reversing these trends."

O'Neill cautioned Congress to take its time with the issue, noting that "haste makes waste in the legislative process." But he also said, "Now is the time for change. Now is the time for reform."

"I believe we can get a bill on the president's desk in the 99th Congress," which ends at the close of next year, he said.

Subcommittee Chairman Charles Rangel, D-N.Y., said he believed it is only the second time O'Neill had testified before a congressional committee. An O'Neill aide said the speaker appeared at the request of Rangel.

In other congressional action:

The House, by a single vote, chopped 31 Corps of Engineers water projects - dubbed "pork barrel" by opponents - from a supplemental appropriations bill for fiscal 1985. The action, on a 203-202 roll call, was a victory for House members attempting to end a traditional buddy system for deciding where dams are built and harbors are deepened. Stripped from the bill were 31 projects that had been approved by Appropriations but had not been authorized by the Public Works and Transportation Committee, as is required by the congressional budget process.

Security measures Two senators, alarmed by the number of espionage arrests in the past year, called on Congress and the administration to tighten access to the country's military secrets. "The Soviet Union and its surrogates have embarked on a massive espionage venture in this country wherein they hope to obtain as much of our classified information as they can," Sens. Sam Nunn, D-Ga., and William Roth, R-Del., said. The pair called for cutting in half the number of people with access to national security secrets. Currently 4 million people have clearances. They recommended tighter controls on classified documents and classifying only essential data. The recommendations also seek more realistic sanctions, such as fines against employees who violate security regulations.

Chemical weapons A Pentagon official warned that congressmen may see leaking chemical weapons moving through their hometowns unless they vote to scrap aging weapons and build safer ones. The Reagan administration has been trying to convince Congress to approve production of new binary chemical weapons in which the deadly nerve gases mix while the bomb or artillery shell is in flight. In the current stockpile of chemical weapons, the gases already are mixed, and at least 900 leak, Thomas Welch said. Congress repeatedly has refused administration requests to resume production of chemical weapons, which President Nixon halted in 1969. If a train carrying current chemical weapons were to crash, Welch said, the results would be "far more lethal than what happened in Bhopal ." A leak of methylisocyanate in Bhopal , India, in December killed about 2,500 people.

Disability reform The Reagan administration is trying to circumvent appeals court rulings on disability reform, lawmakers said. For years Social Security has followed a policy of "non-acquiescence" with some circuit court rulings it disagreed with. It would grant benefits to the person who won the appellate ruling, but not to others in the same circumstances. HHS Secretary Margaret Heckler said Monday that administrative law judges will be empowered to give claimants the benefit of appellate rulings within their circuit. However, state agencies that handle the initial claims will not be authorized to grant benefits based on appellate decisions. Only those who press their case before an administrative law judge will be able to collect. House Social Security subcommittee Chairman James Jones, D-Okla., said the decision "totally ignores what Congress was very specific about last year" in instructing Heckler to comply with rulings her department did not appeal.