Every June an employee puts Form 16 beside twelve payslips, adds up the second, and finds it does not agree with the first. Then they email HR, and HR spends a day working out which number is right.
The certificate is rarely wrong. Something changed after the payslips were issued, and nobody went back to check.
The four usual causes
Arrears paid late. An increment effective in April, processed in July, appears in the July payslip as a lump sum. Form 16 reports it as taxable salary of the year. The payslip and the certificate are both right and they do not obviously agree.
Proofs collected after declarations. In April the employee declared rent and insurance; in January they produced proofs for less than they declared. TDS was recomputed for the last quarter, and the earlier payslips reflect the earlier assumption.
A regime change. An employee who moved between the old and new regime during the year has months computed on two different bases.
Perquisites added at year end. Company accommodation, a car, an interest-free loan — often valued and added in the final quarter rather than month by month.
Reconcile before you issue
The reconciliation is not difficult; it is just never scheduled. Before Form 16 goes out, take the annual gross from the payroll runs, add anything valued at year end, and confirm it equals the salary reported in Part B.
Where it does not, you will find one of the four causes above. Finding it in May takes an hour. Finding it in July, after forty employees have emailed, takes a week and costs you credibility you did not need to spend.
And check Part A actually came from TRACES
Part A must be generated from the TRACES portal on the basis of your filed Form 24Q. A Part A produced from your own payroll system is not valid, however accurate its contents. If your Form 24Q filing is late, your Form 16 will be late — the certificate is downstream of the return, and no amount of payroll readiness changes that.
The underlying fix
Most of this comes from the payslip and the certificate being produced by different processes at different times. When both derive from the same payroll runs, the reconciliation is a check rather than an investigation — and the four causes above show up as visible, dated events rather than as an unexplained gap.