In 1996, the album was repressed on CD and LP formats with new cover artwork and the bonus track "Hekkle and Koch" placed as the album's opener. In 2008, a remastered edition of the album was released, this time with the original 1995 cover art and the removal of both "Hekkle and Koch" and the unlisted hidden track "Touch Me".
Since its release, Black Secret Technology has received widespread acclaim and has been described as a "candidate for "best jungle album ever", as Tim Finney of Pitchfork puts it. Tom Ewing of Freaky Trigger also described it as the "best jungle album ever" and ranked "Finley's Rainbow" as the sixth best single of the 1990s. In 2012, Fact magazine ranked it at number 4 on their list of "The 100 Best Albums of the 1990s."
In a contemporary review, The Guardian gave the album a four out of four star rating, proclaiming that Simpson was "among the first of his peers to corral the acid sound on to a satisfying album. Here, we find him doing precisely for jungle what he helped do for that earlier form. Anyone who's been wondering what all the fuss was about should hear this just to learn what jungle can be in the right hands – enthralling."