John Kelly claimed the controversial executive order was not made to persecute Muslims, but instead to help protect US citizens from potentially deadly terror attacks on their own soil.
Travellers with dual-nationalities woll also be welcomed into the country if they travel on their alternative passport.
He said: “This is not a ban on muslims
“The homeland security mission is to safeguard the american people, our homeland, our values, and our religious liberty is one of our most treasured values.
“It is important to understand there are terrorists and other bad actors who are seeking to infiltrate our homeland every single day.
“It is easier to play defence on the fifty yard line than on the one yard line.
“By preventing terrorists from entering our country we can stop terror attacks striking our homeland.
“We cannot gamble with american lives, and I will not gamble with american lives.
“These orders are a matter of national security and i have sworn responsibility to protect and deend the american people.
A further 872 refugees are expected to be arriving in the US this week and will be processed for waivers.
Travellers with dual citizenship will be able to use their passport from a country other than one of the seven affected by the ban, however.
But officers will be carrying out searches on websites and social media accounts when screening visa applicants.
He said: “We are and will remain in compliance with judicial orders.
“We are and will continue to enforce President Donald Trump’s executive orders with professionalism.
“Our job is to protect the homeland. These executive orders do that.”
“And right now theres a number of countries on the plant that don’t have that kind of record keeping, police-work, that kind of thing.
“The seven in question right now for the most part fall under that category.
“So we are developing what additional vetting, extreme vetting, might look like and we will certainly work with other countries on this.”
Mr Kelly was given his first briefing on the plans as he flew back to Washington from Miami.
But before the plane had touched down – and halfway through the briefing – someone taking part in the call looked up at the television in his office to see the order was already being signed.
On Saturday night a federal judge in New York temporarily blocked the order for citizens who had already arrived in the US and those who were already in transit and held a valid US visa.
And the US Homeland Security vowed to comply with the judicial orders, which would limit part of Mr Trump’s plan to bar all citizens from Iraq, Syria, Iran, Sudan. Libya, Somalia and Yemen from entering in the US for the next 90 days.