Malcolm Green pointed out to the education committee that the recent HMI report on the education service found that, while all secondary heads felt fully engaged with the work of the department, only a "disappointing" half of primary and special school heads did.
Dr Green acknowledged later that the intensive consultations required in renewing Glasgow's secondary buildings had bound schools and the education department more closely together. But he said urgent work was needed to repair links with the primary and special school sectors.
Although it was not mentioned, it is believed that the saga of "ghost pupils" in which a number of primary heads were accused of fiddling their rolls may also have damaged relations.
This issue was not specifically underlined in the council's first formal response to HMI's report, beyond a recognition that "a number of groups of stakeholders felt that communication with them was patchy and could be improved".
The education department will draw up a two-year action plan in response to the report for approval by the committee on September 19.