Brigadier Hugh Monro also said prisoners, particularly those on remand, were not given adequate access to activities.
Prison numbers reached a record 8461 in March, up 469 on the same month last year.
“The year has been marked by overcrowding in prisons, an unwelcome issue which has returned,” said the inspector in his third annual report.
“Scotland’s prisons are coping with record numbers of prisoners and this is bound to affect the access to purposeful activity figures.”
He welcomed the transfer of 114 women to Ratho Hall at Saughton Prison, which has reduced its population to 280, below the 300 recommended following a previous inspection.
Work has also begun on a separation and re-integration unit for difficult prisoners.