Local officials said nearly half of the security forces have been stationed in three schools and students have consequently been shut out.
"Six schools of the 34 in Samarra have been occupied by security forces and three of the six where flattened when suicide bombers attacked the soldiers inside with massive car bombs," said Khalid Hamid, an official at Samarra Education Directorate.
"Some of these six schools were the main centres for baccalaureate examinations [final examinations for high school seniors] and students are obliged to scramble to take their exams in other schools," Hamid said.
"About 200 students are affected as there are not enough classes and desks and we are forced to make some of them take their exams sitting on the ground. The rules do not allow us to have two shifts for the exams because only one set of questions is given to all students," he said.
On 13 June insurgents - presumed to be Sunni militants - blew up two minarets of the revered al-Askariya Shia shrine in Samarra. Its glistening golden dome was blown up in an earlier attack in February 2006 that triggered a wave of sectarian violence which is continuing even now.
"We have to be everywhere as the country is in a war situation and we need to be stationed in empty buildings to protect civilians," said a police officer who asked to remain anonymous as he feared reprisals.
"Schools are the most obvious places for our deployment as we can't be stationed in government buildings which are not empty, or in houses. Some of the schools in which we are deployed are empty as summer holidays have already started for some students, and education officials can easily find alternative places for the others," he added.
"If this situation continues, we will definitely not have enough places for the city's nearly 10,000 students," Hamid added.
The finals, which are the qualifying exams for Iraqi colleges and universities, are being held against a backdrop of unrelenting sectarian violence in Iraq despite a nearly five-month-old US-Iraqi security crackdown.
Ahmed Khalaf, 19, is paying to hire a taxi so he can take his exams in another school.
"My original school is less than 100 metres from my house and now I have to pay at least 4,000 Iraqi dinars (about US $5) a day for the return journey to the other school," Khalaf said.
"I missed out last year as I couldn't take my exams because of the security situation and I'm likely to lose the year again," he added.
Blast-proof concrete walls
In addition, security checkpoints and blast-proof concrete walls are compounding the difficulties faced by Samara residents.
"We don't want them to protect us like this," said Hazim Hassan al-Samaraie, a 44-year-old supermarket owner.
"They completely closed off our street with blast-proof concrete walls, as they are stationed in the nearby school. Two days ago, I couldn't rush my old mother to hospital when she collapsed and we had to put her on a chair and carry her for about 100 metres to where the ambulance was waiting," al-Samarie added.