Spokesperson Thabo Masebe said the president had approved the SAPS Amendment Bill, 2008 and the NPA Amendment Bill, 2008.
Motlanthe recently raised the ire of the ruling ANC by failing to approve the contentious legislation scrapping the Directorate of Special Operations (Scorpions).
He had agreed in December to consider a request by Johannesburg businessman Hugh Glenister to submit legislation disbanding the Scorpions to the Constitutional Court.
Glenister, who went to court unsuccessfully to block the state's plans to dissolve the elite unit, received a letter from the Presidency's legal services division saying his "submission will be considered before the president signs the bill into law".
It was argued that the bills violated South Africa's obligation as a signatory to the United Nations Convention Against Corruption to maintain independent units to combat corruption.
On Thursday, Glenister's attorney, Kevin Louis, received a letter from the office of the president informing him that Motlanthe had assented to the two bills.
"According to the letter from Advocate Sibongile Sigodi, head of legal and executive services in the Presidency, the president found there 'was no basis for constitutional reservation (of the Bills) as contemplated in Section 79 of the Constitution','" Louis said in a statement.
He could not immediately be reached for further comment.