MPs have accused the Department for Innovation, Universities and Skills of failing to "find its feet" since it was established 18 months ago.
A critical report, released this week by the committee responsible for scrutinising the department, highlights concerns about DIUS' ability to manage its budget and its use of "impenetrable" jargon, which the report says could be an attempt to hide a lack of clear direction.
DIUS was established in June 2007 with a remit to make Britain "one of the best places in the world for science, research and innovation".
But the Innovation, Universities, Science and Skills Committee (IUSS) report says it is unclear whether it will achieve its objectives or how the £1.5 billion efficiency savings it promised by 2010-11 will be generated.
The committee claims it experienced "frustrations" in scrutinising DIUS' finances. It says costs could not be compared easily with predecessor departments and reports "a number of concerns" about budget management, including the withdrawal of £100 million for students with degrees studying for equivalent or lower qualifications, science budget allocations and the movement of resources between the Government's Train to Gain programme and student support.
"We noted what may be an emerging pattern of underused resources from further education and skills programmes going to meet spending pressures from higher education," the report says.
IUSS branded DIUS' first departmental report "substandard". It highlights data errors, describes it as "peppered with jargon" and criticises it for containing "assumptions backed up with no clear evidence". It calls for DIUS statistics to be reviewed independently.
The report also examines the work of John Beddington, the Government's chief scientific adviser, who took up the post a year ago.
Giving evidence before the committee in November, Professor Beddington said he saw "no evidence" that homoeopathy worked. But the committee says that in a follow-up note he "chose to offer a selection of papers purporting to provide evidence that homoeopathy may be effective" and "did not ... state that what was important was the balance of scientific evidence".
"We are surprised that rather than champion evidence-based science ... he appears to see his role as defending government policy or ... explaining why there is no clear government policy," the report says.
The IUSS also says that the examples DIUS gives about innovation within its own operations are disappointing. These include the use of new social media, hot-desking and remote working. "For many (this is) far from new," the report says.
A DIUS spokesman said that a recent capability review found it had been successful in creating a new department in a challenging environment.
A spokesman for Professor Beddington said that it was his job to ensure that new policy is based on the best possible scientific evidence available at the time.
"There will ... be times when contradictions exist between scientific advice and other policy imperatives but the chief scientist has and will continue to challenge policy on scientific grounds when he feels it is right to do so ... scientific advice is not the only factor ministers take into account."
TOP CIVIL SERVANT RETIRES
The director-general for higher education in the Department for Innovation, Universities and Skills is quitting the Civil Service after more than 30 years.
Ruth Thompson will be retiring "to pursue other interests and opportunities" on 3 April, after just under two years in the job.
Dr Thompson stepped up from her previous role as director of higher education strategy after the departure of Sir Alan Wilson, former vice-chancellor of the University of Leeds, who left to become master of Corpus Christi College, Cambridge.
In her earlier job, Dr Thompson was responsible for the government target of "moving towards" 50 per cent of all 18- to 30-year-olds having experience of higher education.
At a conference last year she appeared to admit that some people within Whitehall had never believed the target would be hit by 2010, the deadline set in Labour's 2001 general election manifesto.