Hertfordshire County Council last month approved Veolia's plans for the facility at New Barnfield in Hatfield, which is intended to treat municipal, commercial, industrial and healthcare.
But now Pickles has issued an Article 25 notice for the application, indefinitely extending his 21-day window to decide whether an application should be called in for his determination.
The Hatfield plans would see the construction of a dome-shaped building that would comprise mechanical pre-treatment, energy recovery, bulking/transfer facilities and an administration/visitor centre on a 12.6-hectare site.
As Planning reported last month, Welwyn Hatfield MP Mr Shapps wrote to the communities secretary urging him to call in the plans, arguing that the decision process leading to their approval had been "faulty".
Welwyn Hatfield Borough Council also "strongly opposes" the proposals.
Meanwhile, it has emerged this week that football club Tranmere Rovers' plans to build up to 90 homes on a former playing field in Birkenhead have also been hit with an Article 25 notice.
Wirral Borough Council last month approved the proposals for Ingleborough Field, which is a memorial site for the site for 88 former pupils of the Birkenhead Institute who died in World War I.
A Department for Communities and Local Government spokesman confirmed that both applications had been subjected to Article 25 "stop" notifications.