Natural England said growers have been missing deadlines to renew their Entry Level Stewardship (ELS) agreements, which it runs for Defra. Agreement holders receive around £4,000 a year for schemes such as reducing use of fertiliser.
Robin Tucker, a Natural England executive director, said many farmers had missed the latest renewal date, in June.
"It looks like some applications will arrive too late for their new agreement to carry on from the old one. It is vital that intentions to renew are turned into early action to apply. Signing up at the earliest opportunity not only makes sound financial sense, it is also one key to the success of conserving our countryside."
This is the fifth year of ELS and around 12,000 agreements are due for renewal this year, worth a total of more than £200m.
Meanwhile, the NFU has called on Defra to challenge the European Commission after it threatened the department with fines on the environmental scheme.
The commission wants payments to be made in one go rather than throughout the year, and this would delay payments, according to president Peter Kendall. "This situation could seriously compromise the cash flow of many farmers and growers," he explained.