Tim Davies-Pugh, the fund's deputy director of programme management, has written to all applicants to inform them of an increase in the amount of cash available in the first round of funding, from the advertised £60m to £93m.
Mark McGann, deputy director of policy at the fund, said his department decided to cut the number of rounds after it realised that most organisations eligible to apply have already done so. He denied the changes had been made in an attempt to stave off administrative delays in processing and awarding grants.
"The decision was not related to the time we have to process applications," he said. "We believe we have the majority of applications in, so we need to load the money accordingly. Before the fund opened, we estimated that we would receive 800 applications for the first round, but we have received 1,000."
One source told Third Sector that some organisations were likely to be disadvantaged by the changes after waiting to apply and assuming there would be significant funding available in years two and three.
McGann said the fund was keen not to disadvantage such organisations and would make further announcements in the New Year detailing the timetable for applications.
The programme opened to applicants in March, with offers of grants of up to £500,000 for projects that boost infrastructure support for voluntary and community sector bodies in England. The first round closed in June, with the second due to open next summer.
McGann added that another programme, the £50m Advice Plus fund, is still on track to award funds over the advertised three-year period. The fund is open to projects that benefit people who need advice.