The waivers, granted by the State Department and the Department of Homeland Security (DHS), came amid global protests against Trump's rushed executive order.
More than 100 travelers from the countries included in the travel ban, Iran, Iraq, Syria, Sudan, Somalia, Libya and Yemen, were detained, deported or blocked from boarding flights to the U.S.
"We did know the executive order was coming", Kelly said at a news conference, NBC News reports.
"The seven countries named in the executive order are those designated by Congress in the Obama administration as requiring additional security when making decisions about who comes into our homeland", he said. "That is why my office will be filing to join the federal lawsuit against President Trump and his administration".
The imposed ban has resulted in widespread demonstrations at airports across the country.
In spite of President Trump's executive order temporarily halting America's refugee program, 872 refugees will still arrive in the US this week.
Yet this is essentially what's occurred with Trump's executive order. "We had people involved in the general drafting of it". Acting Attorney General Sally Yates, a 27-year Department of Justice veteran, was sacked from her position by the Trump administration on Monday evening after stating that she refused to legally defend the executive order.
"To be clear, this is not a Muslim ban, as the media is falsely reporting", Trump said.
"Over the weekend, individuals - some of whom have been lawful permanent residents for decades - were found stranded outside the United States, leaving families in turmoil".
Secretary Kelly has reportedly met with chairs and ranking members of relevant committees.
Acting U.S. Customs and Border Patrol Commissioner Kevin McAleenan described the process by which the department scrambled to comply with the president's order on refugees just days earlier.
-"The manner in which the Department of Homeland Security is complying with the various court-issued stays of removal, including the number of individuals who have been provided access to counsel".
The letter concludes by nothing that for decades, both Democratic and Republican presidents have backed granting safe haven to families fleeing persecution, violence, terror sexual slavery and torture.