A third of primary schools and a quarter of secondary schools had to re-advertise headteacher posts at least once.
And recruitment is likely to become worse because thousands of school leaders are due to retire within the next 10 years.
The study, by Education Data Services, which uses The TES as its main source, found that the number of advertisements for heads remained at around 2,500, similar to the previous 10 years.
However, many schools continued to experience problems in finding a suitable candidate.
Church schools, those in London and small rural schools were worst affected. The report also found that the pool of eligible deputies was "worryingly small".
January and February 2003 were record months for the number of headship posts advertised, with a total of 714.
However, in April there were only 148 vacant posts advertised - the lowest for any April since 1993.
The number of posts not filled remained at more than 50 per cent for Roman Catholic schools.
John Howson, director of EDS, said: "The problems with recruitment are down to the ageing profile of the population and a lack of the right calibre people coming through who want to be promoted to that level.
"When we had powerful LEAs they were able to manage recruitment and move people around. Schools have been left increasingly on their own."
The best time to recruit was between January and the end of the March, when schools had the best chance of finding their ideal candidate first time around. Autumn ads had the lowest chance of success.
The study also found big variations across the regions. In Yorkshire and Humberside, a record 25 per cent of posts had to be re-advertised, while in the South-east the figure reached 40 per cent for the first time. The biggest drop in re-advertisement rates was in the East Midlands, down from 29 to 20 per cent.
In inner London there was a 3-point decline to 42 per cent. This is thought to be because of the new pay scale for the region.
There was a sharp fall in the number of ads for deputy head posts during 2003. There were 2,277 ads compared with 2,697 in 2002 and 2,930 in 2001.
Around a fifth had to be re-advertised, down from 24 per cent a year earlier.
However, there was an increase of 10 per cent in the number of vacancies for assistant heads. Schools are not required to advertise these posts nationally so the true figure is not known.