Discrepancies in the data have led to problems in the implementation of PM-KISAN scheme, which guarantees income support of Rs 6,000 per annum to eligible farmers.
A large section of farmers, estimated to be around 1.3 crore, have been left out due to data problems.
The chief secretary's letter points out that the information of 1.11 crore farmers in UP, uploaded on the centre's portal, is incorrect.
Names of the farmers, mentioned on the portal, do not match with the name written on their Aadhaar cards.
If this is not rectified, farmers will not be able to get their fourth installment of Rs 2,000.
The letter further says that the bank account details of at least 20 lakh farmers are incorrect and were subsequently rejected by the Public Financial Management System (PFMC).
UP Chief Minister Yogi Adityanath has already expressed dissatisfaction over the slow redressal of the loopholes in the implementation of PM's flagship project in the country's most populous state.
PM-KISAN scheme was announced by former Union Finance Minister Piyush Goyal in February this year.
Under the scheme, all small and marginal farmers are eligible to get Rs 6,000 every year in three installments as minimum income support.
The scheme was launched by Prime Minister Narendra Modi in Gorakhpur ahead of the Lok Sabha elections by transferring the first installment of Rs 2,000 each to more than 1 crore farmers.
( With inputs from IANS )