House-senate conferees set to work yesterday on the $16 billion supplemental appropriation bill needed to keep a long list of federal agencies going during the last three months of this fiscal year. Leaders said the bill must be agreed to before Congress starts its 2 1/2 week recess, scheduled to begin tonight. The House and Senate versions of the bill are far apart.

Rep. Robert E. Bauman (R-Md.). tried to instruct House conferees to reject a Senate provision adding this year's foreign aid appropriation bill to the supplemental. It has been stuck in conference since last year. Bauman protested that approval of the bill would add $1 billion to foreign aid spending this year because, without a bill, the program has been forced to operate at last year's lower spending level. The House ejected his proposal, 249 to 163.

The House and Senate versions of the bill are almost the same in total dollars, but the Senate added several billion dollars to the House bill and then cut several billion from other programs to make room for the increases. For instance, the Senate added $1 billion for foreign aid and appropriated $1.5 billion to the Treasury to guarantee Chrysler Corp. loans. Then it cut $1.2 billion to buy oil for the strategic Petroleum reserve and $400 million from the unemployment trust fund.