The call came after figures showed one council had secured convictions in fewer than 5% of court cases.
Since 2007, education officials at North Lanarkshire Council have taken 74 parents to court because their children had failed to show up for school – but only three parents have been convicted. In the last three years no convictions have been secured despite 43 cases coming to court.
School Leaders Scotland (SLS), which represents secondary school headteachers, said taking parents to court was "time-consuming, bureaucratic and ineffective".
Ken Cunningham, general secretary of SLS, said: "We would like to see local authorities being able to adopt a more flexible approach, rather than being in the position of pursuing court every time or never being able to use the courts."
Mr Cunningham said reasons for truanting were varied and urged schools to look at the context of each case.
"Clearly, taking parents to court has proved hugely time-consuming, bureaucratic and the end result is ineffective," he added.
Jane Liddell, North Lanarkshire head of education quality and development, said: "School provides young people with the best possible chance in life and all parents have a legal duty to ensure their children attend. We have been actively pursuing parents whose children fail to attend, but with little success in the courts. The service continues to review its processes to improve school attendance."
Councils are currently obliged to opt either for a truancy policy – like North Lanarkshire's – that sees parents of wayward pupils taken to court, or one that requires them to implement alternative strategies.