Pupils in Edinburgh were cut off from revision resources ahead of key exam dates after an attempted cyber attack on the council's education department.
Staff spotted a suspicious invitation to a meeting earlier on Friday and realised it was "spear-phishing" – which impersonates a trusted source.
Parents were sent texts telling them that students' passwords have been reset as a precaution – meaning pupils studying for exams no longer had access to their school's learning resources.
Pupils have been going into schools to be given new passwords.
On Friday night, the council said pupils preparing for exams would be given priority support following what it called a "difficult but necessary" decision.
It follows a suspected criminal ransomware cyberattack on schools in West Lothian earlier this week.
Edinburgh Council's education, children and families convener James Dalgleish said staff spotted "unusual and suspicious activity" on the schools and early years IT network.
"As a result, we took the precautionary decision to immediately reset passwords for all users across our education service," he said.
Councillor Dalgleish told BBC Scotland News the phishing attack was spotted very quickly by council officers and some networks were immediately shut down.
"That's obviously unfortunate and a distraction for some pupils who are going through their exam processes but it was necessary to make sure we have the integrity of our educational infrastructure," he said.
"That's not been compromised in any way."
He added that council officers were very well trained in recognising phishing attacks and said investigations into the incident would continue.
As well as pupils being given new passwords, all revision materials have been put on the council website.
"I want to thanks parents and pupils for being patient with us as well as the teachers for opening the secondary schools this morning," he added.
The council believes everything should be back to normal on Monday.
Councillor Dalgleish said the Scottish Qualifications Authority (SQA) had been informed and any pupils with concerns should speak to their teachers.
