Chris Brown, head of Norwich School and chairman of the Choir Schools Association (CSA), told its annual conference that the decline in singing in school and the drop in regular church-going also made recruitment more difficult.
In 1997, 521 children tried for 200 places in the association's 40 schools. In 1986, there were 679 candidates for 191 places.
Girls seem to be more eager to become choristers than boys, although only five schools - Salisbury, Wells, Exeter, York and Ripon - admit them in such a role. There were 96 candidates last year for 25 vacancies for girls. Other cathedrals, such as Norwich, Rochester, Bristol and Wakefield, have girls' choirs but they are not offered singing places at the schools.
Mr Brown told choir-school heads at St Paul's Cathedral School in London: "There are other distractions for young people; they are less used to singing in school yet more music of all kinds is available to them at every turn. Fewer families regularly go to church and the commitments expected of choristers are considerable.
"To meet the challenges of recruitment in an increasingly secular society... choir-school heads and cathedral foundations must do all in their power to draw attention to what is offered and to encourage singing."
Richard Shephard, head of the Minster School in York and the association's treasurer, said: "Before the last war, queues of hopeful parents and children used to wind down Deangate in York when the chorister trials were on. The situation nationally for chorister recruitment is not so brilliant." He said computer games were partly to blame.
Both he and Mr Brown emphasised, however, that although the competition for places had dropped, the quality of choirs was higher.
Mr Brown said people feared that they would not be able to afford the fees for their children, but bursaries from schools and the Government meant many choristers had all their fees paid and most had at least half paid. The average cost of a chorister's tuition and accommodation at CSA schools is pounds 1,900 a term. But cathedrals help with funds for scholarships from the Dean and Chapter, and the Government offers pounds 120,000 a year for means-tested bursaries.
A spokeswoman for the CSA said: "Figures suggest that only six children were lost to the system last year because there was no way the money could be found. But that is still six too many."
Stephen Oliver, precentor of St Paul's Cathedral, said the standard of choral music was higher than at any time in living memory, thanks in part to broadcasts on television and radio.
"Thirty years ago, the choristers practised singing and music but there was little rehearsal. Today there is much more rehearsal to reach such high standards."
The tradition of male choirs stretches back more than 400 years. The addition of females voices is relatively new, but the lack of funding, pressures of the national curriculum and a demand for equal opportunities have forced them to admit increasing numbers of girls.
However, even where girls have been allowed in, they rarely sing with the boys, but in separate choirs at separate services, due to a received wisdom that boys perform less well in front of the opposite sex. St Mary's Cathedral choir in Edinburgh is a rare exception in blending the two since 1978.
There are both state and independent schools within the CSA. Some are preps catering for children from seven to thirteen, and most include children outside their choirs; Westminster Abbey Choir School is the only one just for choristers.