A House-Senate conference committee yesterday cleared away one of the last big obstacles to a new farm bill, but in so doing added costs that further threaten the measure.

With an agreement on loan rates and target prices for wheat, corn and other grains, the bill's estimated price tag rose another $440 million-- putting it well beyond the White House's announced toleration limits.

Department of Agriculture officials calculated that the measure is now about $600 million over the $10.6 billion level of the Senate version, which President Reagan said he hoped the conferees would abide by.

The conference leaders, Sen. Jesse Helms (R-N.C.) and Rep. E (Kika) de la Garza (D-Tex.), indicated again yesterday, however, that they intend to return to other sections of the bill in an attempt to trim costs.

In the first of the reopeners, the conferees last night agreed to cut the peanut loan level from $580 a ton to $565, with a 6 percent lid on annual increases. But the changes were expected to have little budget impact, because peanut lobbyists contended the program would go on at no cost to the government.

In another attempt to mollify critics, the conferees agreed to cut the fiscal 1982 price support for sugar from 18 cents a pound to 17.5 cents a pound. As with peanuts, the move was expected to have no effect on federal expenditures.

Among other sections ticketed for a second look were dairy supports and embargo protections.

Agriculture Secretary John R. Block insists that the dairy price support section is unacceptable.

But wheat and feed grains, by agreement of the conferees, will be exempt from the scheduled cost review--a demand laid down by House delegates who had compromised repeatedly on price levels for those commodities.

The agreement sets the price support loan rate for wheat at $3.55 a bushel through 1985, with a target price of $4.05 for 1982, with annual increases not to exceed 6 percent. The current loan rate is $3.20; the target is $3.81.

Corn support loans would be set at $2.60 through 1985; the target would start at $2.70 this year and move up 6 percent annually. The current target price--a direct subsidy payment to farmers--is $2.40.

Among the major commodities, the agreement on wheat, corn and feed grains such as sorghum, barley and oats was the most nettlesome. The conferees had been divided for two weeks, arguing almost daily over nickels and dimes.

But in the administration's ledger books, the nickels and dimes meant big bucks. USDA lobbyists insisted that the conference deflate the loan and target price rates.

Yesterday's grain agreement-- more than the Senate wanted, less than the House demanded--left all sides sour. Rep. Ron Marlenee (R-Mont.), a conferee, said that the agreement "betrayed" farmers and that he would vote against the bill .

The conference today faces sharp disgreement about more food stamp cuts proposed by Helms.