The warning came as US began accepting employers' H-1B visa petitions for next fiscal year.
The Trump administration has warned companies against "misusing" the H-1B work visas programme - sought most by Indian IT firms and professionals - and discriminating against American workers.
"The Justice Department will not tolerate employers misusing the H-1B visa process to discriminate against US workers," said Acting Assistant Attorney General Tom Wheeler of the Civil Rights Division.
The White House has also warned against abuse and fraud of H-1B visas by companies.
"The Trump Administration will be enforcing laws protecting American workers from discriminating hiring practices," White House Press Secretary Sean Spicer told reporters at his daily news conference.
The warnings came as the government began accepting employers' H-1B visa petitions for the next fiscal year beginning October 1.
The US Citizenship and Immigration Services (USCIS) yesterday also announced multiple measures to "deter and detect" what it described as "fraud and abuse" of H-1B work visas.
The US announcement indicated that its government will be tough in approval of H-1B visas this year.
The USCIS has a Congressional mandate to issue 65,000 H-1B visas in the general category and another 20,000 for applicants from US universities in science, technology, engineering and mathematics.
Asserting that its multiple measures will further "deter and detect H-1B visa fraud and abuse", the USCIS said the H-1B visa programme should help US companies recruit highly-skilled foreign nationals when there is a shortage of qualified workers in the country.
"Yet, too many American workers who are as qualified, willing and deserving to work in these fields have been ignored or unfairly disadvantaged. Protecting American workers by combating fraud in our employment-based immigration programs is a priority for the USCIS," a statement said.
The H-1B visa programme allows US companies to temporarily employ foreign workers in specialty occupations such as science and IT.
Indian tech giants like TCS, Infosys and Wipro are among the major beneficiaries of H-1B visas.
During his election campaign, President Donald Trump had promised to increase scrutiny on the H-1B and L-1 visa programmes.
The anti-discrimination provision of the Immigration and Nationality Act (INA) generally prohibits employers from discriminating against US workers because of their citizenship or national origin in hiring, firing and recruiting.
"Employers violate the INA if they have a discriminatory hiring preference that favours H-1B visa holders over US workers," the Justice Department said in a statement.
"US workers should not be placed in a disfavoured status, and the department is wholeheartedly committed to investigating and vigorously prosecuting these claims,"
Tom Wheeler warned.
The USCIS has also announced an email helpline against abuse and fraud of H-1B visas. It says it will make unannounced site visits to H-1B petitioners and their employees.
The site visits are not meant to target non-immigrant employees but rather to identify employers who are abusing the system, it said.