A 33-year-old Iranian national and a 24-year-old British man were arrested in Manchester on Wednesday evening.
A National Crime Agency spokeswoman said: "NCA officers have tonight arrested a 33-year-old Iranian national and a 24-year-old British man in Manchester, on suspicion of arranging the illegal movement of migrants across the English Channel into the UK.
MORE REGIONAL NEWS>>> Manchester stabbings: Terror suspect arrested after 'frenzied' New Year's Eve knife attack detained under the mental health act"As the investigation is ongoing, we are unable to comment further at this time."
The arrests come as it was revealed Home Secretary Sajid Javid had written to the Ministry of Defence to request use of the Royal Navy.
An MoD source told the Press Association that HMS Mersey, an offshore patrol vessel, is "available and ready" to be deployed.
It would represent a significant escalation of Britain's response to the migrantion issue after Mr Javid earlier this week announced the redeployment of two Border Force cutters from the Mediterranean.
A Ministry of Defence spokesman said: "Our Armed Forces stand ready to provide additional capacity and expertise to assist the Home Office with the response to migrant crossings. Royal Navy ships continue to conduct patrols to protect the integrity of UK territorial waters."
On Wednesday Mr Javid was criticised for questioning whether migrants using small boats to make risky journeys across the English Channel are genuine asylum seekers.
Speaking on a visit to Dover he said: "A question has to be asked: if you are a genuine asylum seeker, why have you not sought asylum in the first safe country you arrived in?"
He also suggested those picked up by UK authorities faced having asylum requests denied as a deterrent to prevent others undertaking the same dangerous journey.
Foreign Secretary Jeremy Hunt said Mr Javid was right to say that the UK's "proud tradition" of granting asylum is not abused.
The Home Secretary, who cut short a family holiday in South Africa to take personal control of the situation following criticism of the Government's response, defended describing it as a "major incident".
He told reporters 539 people had crossed the Straits in 2018, with 80% making the journey in the last three months of the year.
Labour backbencher Stella Creasy, who has visited migrant camps in Calais, accused Mr Javid of normalising "anti-refugee rhetoric online".
She added: "The asylum system in France is completely deadlocked and I fear deliberately so - they should be challenged on that.
"But none of that means Britain can absolve itself of responsibility to refugees.
"People will continue to die and be at mercy of traffickers all the time politicians pretend to play tough for votes rather than recognise why people flee."
Paul Hook, head of campaigns at the charity Refugee Action, added: "The Home Secretary must remember that these are people who have fled their homes and they each deserve a decent, humanitarian, and understanding response.
"This situation demands our compassion and cool, calm heads and we hope the Home Secretary will reflect this in his statements on the subject."
Dr Lisa Doyle, director of advocacy at the Refugee Council, said Mr Javid's comments were "deeply concerning".
She added: "The outcome of an asylum application cannot be pre-judged before it has been made and must be processed on its individual merit, irrespective of how that person reached the country."
While on a visit to Malaysia, Mr Hunt was asked if he shared Mr Javid's suggestion that those attempting the crossing may not be genuine asylum seekers.
"I think the Home Secretary is right to say that, as a country that is very proud of our tradition of granting asylum to people who need it, we also want to make sure that isn't abused," he said.
"But our priority right now is the safety of people in the Channel; to discourage people from making this very dangerous crossing, but to make sure that everyone that does is kept safe."