Although the Reagan administration hasn't had much success getting some of its user fee proposals through Congress, federal agencies continue to increase the fees that they control.

Aliens who are turned down the first time they try to become naturalized citizens or avert deportation will have to pay more to stay here. The Immigration and Naturalization Service has recommended 34 new or higher fees, including a $110 charge to bring a case before the Board of Immigration Appeals or to seek a stay of a deportation or exclusion order. (The old fees used to be $50 and $70, respectively.) The INS said in a Federal Register notice that it actually costs the government $691.59 to process one of these applications, but said, "If the fee were set to recover the government's costs, it would likely chill the right of appeal of some meritorious cases." It added: "The fee should not be so low as to encourage frivolous appeals, but not so high as to discourage legitimate ones." The agency is accepting comments through Sept. 27.

* The Federal Energy Regulatory Commission has proposed stiff new fees that natural gas companies would have to pay when they want to be certified by the agency or increase their rates. The basic charge for an application for a hearing will be $8,800; it will cost $63,300 to have staff members lay the groundwork for the hearing and then $54,500 for the hearing itself. The agency is accepting comments through Nov. 9.

* Gaining the "USDA" seal of approval is going to cost meat and poulty processors, and probably some consumers, more money. The Agriculture Department's Food Safety and Inspection Service has recommended a 13.6 percent increase (to $16.68 per hour) in the fees for regular inspection and certification services and for overtime duty (to $19.40 per hour). Comments are being accepted through Sept. 28.