The Newcastle-based company, which has 1,681 shops, said the adverse weather in January and March was a big factor in a 4.4% drop in like-for-like sales in the 17 weeks to Saturday.
Whilst trading in the past two weeks has shown an improved trend, it said profits were currently running short of last year and against its own hopes.
The update triggered an 8% fall in the company's share price as Greggs said profits for this year were now unlikely to meet the current range of City expectations of between £47.5 million and £55.2 million.
The company warned: "We do not expect a significant improvement in the difficult underlying market conditions in the short term."
As well as the poor weather, Greggs has experienced lower footfall across much of its estate. It has attempted to offset pressure on its high street locations by focusing new openings on workplaces, travel and leisure destinations.
It has opened 18 new shops so far this year, including six franchised units with motorway services operator Moto. It has also completed 59 refurbishments in the period but closed eight shops.