"That's why I don't get overly excited with the House bill right now because it's not going to pass in the Senate", he said.
Trump is asking Congress for a permanent solution as the U.S. is running out of resources to keep families together.
US lawmakers in the lower house resoundingly defeated an immigration reform bill on Wednesday with the so-called moderate legislation coming from the Republican leadership and supported by President Donald Trump.
The bill was killed 301-121, with almost half of Republicans opposing the measure.
The roll call seemed to empower GOP conservatives on the fraught issue. The vote count shows the deep gulf between conservative and moderate Republicans. But he made clear that his agency is working with the Department of Justice to figure out a way to continue criminally charging all illegal border crossers while keeping them detained with their children.
Late on Tuesday, U.S. District Judge Dana Sabraw in San Diego blocked the administration from separating families at the border, and ordered that those who were separated be reunited within 30 days, a decision the American Civil Liberties Union hailed as a "complete victory". "Will we step up to be the country that allowed me, as a young boy, to find safety with my mother and father?"
The House rejected the GOP's second attempt at passing immigration reform Wednesday, clearing the way for a possible vote on a narrower proposal to codify the Trump administration's family separation policy next month.
But that seemed unlikely.
Democrats and immigration activists said the vote proves that only a bipartisan compromise between Democrats and Republicans could become law.More news: Germany leaves Russian Federation after crashing out of the World Cup
The broader bill includes trade-offs, including a multi-year path to citizenship for young immigrants who have been living in the USA illegally since childhood and $25 billion for Trump's border wall.
But the states say his order is riddled with caveats and fails to reunite parents and children who have already been torn apart.
Last week he even tweeted urging the House to "stop wasting their time" on an immigration bill until after the midterm elections.
The tweet - which referenced Rep. Even Donald Trump's endorsement failed to eliminate the deep division within the caucus on a bill that probably had no chance in the Senate anyway.
In an executive order ending the family separations, Trump did not explain how his hardline immigration policies could be adjusted to keep families intact and house them while their legal status is assessed. The bill had criminalised the process and suggested deportation of 40 to 50 per cent of unauthorised immigrants who entered via a visa. But conservatives relish such tough stances.
The U.S. Chamber of Commerce also expressed disappointment with the vote. And that assumes it gets more than the 121 votes the most recent bill got on Wednesday.
Rep. Peter Welch voted against both immigration measures.
This spring they launched a petition that could have led to House passage of liberal-leaning measures creating a pathway to citizenship, bills backed by Democrats but opposed by most Republicans.
The bill also sought to address the issue of children being separated by their parents at the border by allowing the government to detain families together.