Director general of the Serious Organised Crime Agency (Soca) Bill Hughes, poured scorn on a "small number" of staff who have gone public with concerns about the organisation's success rate.
Soca's chairman Sir Stephen Lander also admitted that it was spending less time and money combating drugs because of the competing demands of other crimes, such as gun and people trafficking.
Sir Stephen, a former head of MI5, also revealed that Soca bosses had been forced to crack down on "Spanish practices" by some staff - who came from police, Customs and other law enforcement agencies - such as bumping up overtime hours.
Opposition politicians said the comments by the two Soca chiefs showed the secretive £407 million-a-year agency is actually damaging the fight against crime.
Liberal Democrat home affairs spokesman Chris Huhne said: "Sadly, Soca's performance in fighting organised crime suggests that it is a problem, not part of the solution.
"Stephen Lander's attacks on his colleagues for so called 'Spanish practices' shows this is an agency in complete turmoil.
"The Home Secretary must insist on a better return for the public's £400 million. Otherwise she will have to go back to the drawing board and re-examine the skills and teams needed to tackle global crime."
Shadow home secretary David Davis said: "The Government set up Soca amidst great fanfare, with the pledge to sharply improve its performance in the fight against organised crime.
"Yet Soca has not had a dramatic effect - and in some areas, is performing worse.
"Two years on, after nearly a billion pounds' worth of investment and 4,000 officers, Soca is convicting fewer Mr Bigs than its predecessor, missing most of its targets for asset-seizing and cannot identify the amount of drugs seized abroad destined for the UK.
"Nor is there much evidence of Soca cracking down on a range of other serious threats - including gun crime, human trafficking and cyber-crime."
The comments by Sir Stephen and Mr Hughes followed reports in a national newspaper this week in which Soca staff criticised what they claimed was a top-heavy management structure and a failure to arrest crime lords on the agency's hit list.
Mr Hughes said: "There are some disgruntled people. It is a very small number.
"If they have something to say to us there are routes to do it.
"To do it in the way they are doing it is to denigrate their colleagues and is disgraceful."
Sir Stephen, launching Soca's annual report, said: "There has been an issue about our quota of overtime.
"We were trying to bear down on some Spanish practices that we inherited such as putting off starting a job back to 4pm so you get overtime.
"I don't buy what has been said about the management team. I believe we have the right size of management team."
Mr Hughes admitted that some members of Soca's 4,000-strong workforce had been more comfortable in the agencies which preceded its creation in 2006.
The annual report revealed Soca has reduced the amount of work done to combat drugs on Britain's streets.
It also admitted that success in tackling the heroin problem had been "more elusive" than achievements against cocaine and other drugs.
Two tonnes of heroin were seized by the agency in 2007/08, up half a tonne, but 84 tonnes of cocaine were impounded in the same period, a 20% rise.
The number of operations and projects mounted by Soca against Class A drugs last year was 195 compared with 215 the year before.
Work against hard drugs took up 55% of the organisation's time and effort, down 5% on the previous 12 months.
Instead, more effort was dedicated to detecting firearm-related threats (up from 1% of Soca's effort to 4%) and organised immigration crime (up 1% to 12%).
Sir Stephen said of the agency's targets: "The reason we're rolling down the overall number of projects and activity on drugs is because we are trying to build on other ones.
"We have been shifting priority because that is what we have been asked to do."
The report acknowledged that the agency faced a challenge to extend its impact on different types of crime "without any growth in the workforce".
Mr Hughes revealed that Soca was currently running 18 operations against gun crime, including one against internet-based firearm sales, and another targeting a US-based company dealing with British customers.
The agency is also increasing work to stop crime lords continuing to operate their empires from inside jail, Mr Hughes said.
He cited the case of one criminal who was moved from an open jail back to a secure one in a bid to hinder him carrying out such activities.
On the claims by some Soca staff earlier this week that the agency had not arrested any of its 130 key targets, Mr Hughes said in fact 36 had been detained, with possibly more arrests awaited overseas.
"The allegation that we are not pursuing criminals is total rubbish," he said.
"I'm surprised that anyone gives credence to it."
In all, almost 90 tonnes of Class A drugs were seized with Soca partners at home and overseas, the report said.
However, the number of ecstasy pills seized fell from 4.4 million to one million year-on-year and no doses of LSD were seized, compared with one million in the previous 12 months.
Cannabis confiscations tripled to 30 tonnes.
More than 2,000 serious organised criminals were arrested due to Soca work during the year, it added.
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