The RTI scheme was due to come into force next month (Grower, 1 March).
HM Revenue & Customs announced last week that businesses with fewer than 50 employees that currently run their payroll monthly but pay more frequently will not have to report any more frequently than monthly for at least the next six months.
The NFU has been involved in "a series of robust but constructive discussions" with HMRC.
NFU head of tax Michael Parker said: "This is a very positive step and we expect it will significantly ease the introduction of RTI for many businesses. We now look forward to working with HMRC to find ways of improving real-time reporting beyond the next six months."
HMRC representatives have undertaken to work with employer representatives over the summer to find ways of making real-time reporting more practicable.
Federation of Small Businesses representative Robert Downes added: "This development perhaps hints at something of a panic at HMRC that many small firms still aren't fully prepared for RTI.
"However, this does seem the sensible course of action because a tax system in meltdown come April is in nobody's interest."