The National Audit Office issued the guidance in a report yesterday that confirmed the reluctance of some schools to get involved in the new qualifications for teenagers.
The report, on local preparations for the launch of the new courses from next September, said there was generally strong support in schools, colleges and local authorities for the diplomas.
However, 40 per cent of the clusters of schools, colleges and employers that have been set up to run the diplomas told the auditors that local institutions in their area were not getting involved. League table pressures, it said, led to a belief that higher-performing schools were reluctant to consider working with less successful schools or colleges "in case it affects their results".
The report said: "Local authorities and the Learning and Skills Council should be prepared to use sanctions where necessary in relation to those few institutions that are unwilling to collaborate."
Sanctions could include Ofsted noting the school's unwillingness in its inspection reports, an audit office spokesman said.
The report said the Government should also adapt league tables to reward schools and colleges for working in partnership.
Grammar schools had been expected to be more reluctant than others to offer the diplomas. But the report said there were signs of hesitancy in all types of school.
It found that the Government had so far hit all the development targets or milestones it had set for itself to produce the diplomas. All pupils must be given the chance to study the courses in one of 17 subjects by 2013.
However, employer involvement - a key element of the new work-related courses - appears patchy. Of the 241 diploma consortia surveyed, nearly half had not involved businesses in their planning and more than two-thirds had encountered difficulties arranging the 10 days' work experience required.
"Many employers have not heard about the diplomas," the report said. Universities were also often not closely involved: fewer than one in five of the consortia surveyed had active involvement from higher education.
In a policy paper last month, the Oxford University-based Nuffield Review said the diplomas would not succeed in becoming the qualification of choice for teenagers while A-levels survive. It also said teachers and exam boards had been involved very little in the design of the new courses.
Graham Lane, chairman of the development partnership for the engineering diploma, this week accused the paper's authors of trying to wreck the courses before they started. He said: "When people write a policy paper, it would be helpful if they established the facts before coming to conclusions."