They are battling to meet the deadline - 9 a.m. sharp - to report at office or else they will be marked late and will have to compensate and leave late in the evening.
"Hardly anybody comes late now!" said a smiling security officer outside the ministry office as he hurriedly checked the identities of employees.
The culture of punctuality has developed fast in the P. Chidambaram-led home ministry after the scanners were installed Sep 1 and employees asked to come on time and leave after 5.30 in the evening.
Bureaucrats in India are known for not sticking to time. But the change has begun and Home Minister Chidambaram has taken the lead. The attendance system is his brainchild.
The minister has been able to initiate change in the decades-old work culture of government employees - sarcastically referred to as 'babus' who don't care too much about being dutiful.
On Sep 1, the day the scanners were installed, Chidambaram arrived at his office at 9 in the morning and marked his attendance by placing his index finger on one of the biometric machines.
Following their boss, thousands of the ministry's employees are now doing the same - being punctual. Or else a 10-minute delay thrice a month will be counted as one day's  casual leave.
"It was hard to change the old habit, but one has to do it. There was a traffic jam. Thank god I still made it on time," said an employee requesting he should not be named.
A senior official said: "Earlier employees in the ministry used to come at their own sweet time and leave whenever they liked. But not any more."
There are 18 scanners for about 5,000 employees in three offices of the ministry in Delhi - 10 in  North Block and rest in the Lok Nayak Bhavan and Jaisalmer House offices.
The ministry is to examine the pattern and the performance of employees and working of the new system Sep 15. The first 15-day record will be sent to the administrative division.
Within eight days of installing the scanners, the employees in the ministry have found their own way of reaching on time.
"They come together by car pooling, catching the same buses and alerting each other if anybody gets late," the official said.
The employees who complain of frequent traffic jams on Delhi roads may not be too happy within even if they are abiding by the rules so far, but the punctuality drive has given commoners a reason to smile.
People in India are used to waiting patiently for government employees to come for duty. The lack of punctuality causes huge delays in processing documents.
Chidambaram, while inaugurating the system, said other offices will follow suit. "I hope that people absorb the spirit and the purpose with which this system has been introduced. But this is a message to the whole country that everybody must do his work for the allotted time."
"I understand flexi time, we will introduce some flexibility, but the flexibility is if you come 10 or 15 minutes late, you have to work another 10 or 15 minutes," he had said in his stern message.