Golushko, in his first public statement since Yeltsin disbanded his ministry last week, told reporters that the service could lose 30 percent of its officers when it is transformed into a new counterintelligence service.
Golushko has been named to head the new organization, reporting directly to Yeltsin, instead of parliament and the government, as previously.
Two other long-serving intelligence officials also joined in the criticism.
"I do not denounce the president, I obey him", Reuters quoted Golushko as saying. "But I am talking about the personal feelings of honest officers".
Asked if the reorganization would hurt Russian security, Golushko said: "There is a saying - if you want less efficient work, start reorganizing. But I hope that professionalism and the sense of civic duty of every officer will enable us to restore the full potential shortly".
Yeltsin condemned the ministry last week saying it was the "last bulwark of the former totalitarian system" and it was necessary to "disband an organ which undertook police surveillance of people".
Golushko, a 30-year veteran of the KGB who backed Yeltsin during the Oct. 3-4 White House uprising, acknowledged in October that the Security Ministry was still conducting political investigations.
However, Alexander Mikhailov, a Security Ministry spokesman said that it was the "country's leadership" which was to blame saying that the ministry only did such work under orders.
"The first thing we should do is abolish political investigations", Mikhailov said Monday, referring to tapping phones, spying on people and keeping personal files. "And to abolish this system we need the cooperation of the country's leadership. They should not make requests that we conduct such work. All we do is fulfill orders".
The former intelligence chief of the KGB, Leonid Shebarshin, also criticized Yeltsin's decision, saying that counterintelligence is too closely related to the agency's other services and will lead to fragmentation if split up.
Shebarshin told Obshchaya Gazeta, that Yeltsin's aim of getting rid of the ministry as "an instrument of political surveillance" would not work because the new parliament would not be able to monitor the service if it were split.
Yeltsin made it clear in a press conference last week that a major purge of security personnel would take place under his leadership.
The Security Ministry reorganization was part of a larger reshuffle in the country's administration. On Thursday, Yeltsin decreed that the Itar-Tass news agency will resume its Soviet-era role as the mouthpiece of the Kremlin by restoring some of its state privileges and making it the government's official news agency.
The decree stated that the agency would receive generous benefits from the government and its staff would effectively have the status of state employees. The decree was part of a media shake-up that followed the electoral success of Communists and nationalists.
Earlier last week, the president dissolved the Information Ministry and his Federal Information Center and appointed the "father of glasnost", Alexander Yakovlev, to head the Ostankino television and radio station.
On Friday, Yeltsin continued his sweeping reforms by ordering Prime Minister Viktor Chernomyrdin to cut the staff of the Council of Ministers by 20 percent within a month.
In a separate development, Yeltsin's press service officially confirmed Monday that U. S. President Bill Clinton will visit Russia from Jan. 12-15.
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