Acting Chief Justice Uma Nath Singh, who passed the order yesterday, referred the matter suo moto to a full bench.
He also directed CBI to produce the documents in the next hearing of the case on December 5.
Singh was hearing a PIL filed by an advocate and issued the order for seizure of the buildings' documents on the basis of a report submitted by an eight-member committee constituted by a bench of the HC on September 4 this year.
The committee, which was headed by East Khasi Hills deputy commissioner Sanjay Goyal, had found that of the 52 under-construction buildings in 19 identified areas of the city 12 had violated the bye laws. Its report was filed on October 16 last.
According to MUDA provisions, no private building can exceed the G+3 limit.
On April 11 this year the HC in an interim order had prohibited construction beyond G+3 in Shillong following its concern that there was rampant construction of high-rises in the hilly state and Shillong fell under Seismic Zone 5.