President Reagan vetoed an "urgent" supplemental appropriations bill yesterday for the second time in two days, saying it allocated $1.3 billion more for federal programs than he had requested and therefore "still does not do the job."

In bouncing the emergency spending bill back to Congress, Reagan adopted a somewhat conciliatory tone, expressing extreme disappointment that he had had to do so but asserting that the nation needs "deeds, not just promises to be convinced deficits will be reduced."

White House aides had signaled late Thursday that Reagan would cast a second veto, and before adjourning for the Fourth of July recess, the Democratic-controlled House approved as a precautionary measure a bare-bones, stop-gap bill Reagan could sign to avoid widespread employe layoffs and keep going noncontroversial programs awaiting funds.

Aides to Senate GOP leaders said they were hopeful that the Senate could approve an identical measure next week so that they could send it off to the White House for Reagan's signature and avoid the turmoil that could ensue if they must wait for the House to return from vacation to thrash out differences.

Government employes in jeopardy of being placed on leave without pay next month if a supplemental appropriations bill is not passed include workers at the Economic Development Administration in the Commerce Department, the Merit Systems Protection Board, the Alcohol, Tobacco and Firearms unit in Treasury and those in the inspector general's office of the Health and Human Services Department.

The first supplemental appropriations bill Reagan vetoed Thursday had contained a $3 billion mortgage-interest subsidy program for the housing industry, the only piece of anti-recession legislation this year. Reagan and aides had strongly signaled for weeks that he would veto the bill because of that measure.

But as late as Thursday afternoon, the guidance given reporters at the White House was that it was unlikely Reagan would veto a second bill even though the second bill included the $1.3 billion in additional aid for the Postal Service and flood control, housing, highway construction and job training programs.

But as the House was failing to override the first veto, White House lobbyists were learning that there was enough cut-the-budget sentiment there to sustain a second one. The decision was made that Reagan would cast his sixth veto since in office, a day after the fifth one.

Aides to House Democrats said they would attempt to override the second veto when House members return from their two-week recess. They also said they intended to keep trying to attach the mortgage-interest subsidy program to other legislation.

But the author of the subsidy program, Sen. Richard G. Lugar (R-Ind.), appeared to have given up the fight. He had hoped to persuade Reagan to sign the bill, but he failed.

A spokesman for the National Association of Homebuilders, which had lobbied hard for the housing program, said members of his group plan meetings with members of Congress after the recess and would continue to apply pressure on them for a housing program.

In his second veto of the spending bill yesterday, Reagan said, "A key to lasting economic recovery is to bring interest rates down and keep them down. We can only do that by convincing skeptical markets that this government has the will to control federal spending and borrowing across the board."