"There should be no further releases from Gitmo. These are extremely dangerous people and should not be allowed back onto the battlefield," tweeted Trump.
There are 59 prisoners remaining at the controversial detention center, only a handful of whom have been tried for alleged crimes. Many are in legal limbo.
Obama came to office vowing to shutter the facility, saying detention without trial did not reflect American values.
But he has run up against political and legal hurdles, Pentagon foot dragging and stubborn Republican opposition in Congress.
With Guantanamo's closure blocked, Obama's White House has focused on whittling down the number of inmates.
George W Bush had released or transferred around 500 inmates before leaving office, Obama has released or transferred around 179.
Obama's administration is reportedly eyeing further transfers before Trump is sworn in on January 20 — the president-elect having on the contrary vowed to "load (Guantanamo) up with some bad dudes" once in office.
Around 20 of the remaining inmates have been cleared for release. But finding countries to take them has often proven time consuming.
Trump's declaration is the latest in a series of public disputes between Obama and the outspoken president-elect, who has jettisoned the notion there is "one president at a time.