The prosecution of Michael K. Deaver seems certain to cost taxpayers more than $1 million.

Justice Department officials said it is the second most costly of any of the investigations being handled by the five active independent counsels.

As of Oct. 30, the costs of the staff assembled by Deaver's prosecutor, Whitney North Seymour Jr. of New York, had totaled $842,431. Deaver's trial began Oct. 19 in U.S. District Court and lawyers say total costs should easily exceed $1 million by the time appeals are concluded.

Early in the case Seymour, a former U.S. attorney, put the costs of the actual investigation that preceded Deaver's indictment March 17 at about $300,000. The prosecutor attributed the rest of his bill to the costs of countering the intense pretrial maneuvering and frequent motions filed by Deaver's lawyers.

Deaver's defense team declined to estimate its bill, but individuals familiar with the costs of mounting such a defense in Washington said it could equal the $1 million cost of the prosecution.

The most costly independent investigation, according to Justice spokesman Patrick S. Korten, is that of Lawrence E. Walsh, who for the past year has been directing the criminal inquiry into the Iran-contra affair. The costs of his operation totaled $3.8 million as of Oct. 30, more than half of the $6.3 million total costs of all five independent counsels with active staffs.

Seymour's total was slightly ahead of that of Alexia Morrison, who is looking into allegations of lying by Justice Department officials to Congress about the agency's handling of its investigation of the Environmental Protection Agency's Superfund program. Her investigation had cost $832,464 as of Oct. 30.

James McKay, who is investigating Attorney General Edwin Meese III and former White House aide Lyn Nofziger, had run up a $795,429 tab. The smallest bill was $21,035 incurred by an undisclosed lawyer who was named in a sealed order to investigate an income tax issue involving former assistant attorney general W. Lawrence Wallace.