The end of a controversial Italian navy operation that is rescuing thousands of asylum seekers in the Mediterranean is likely to result in many more deaths at sea, according to human rights groups.

Operation Mare Nostrum has picked up more than 140,000 asylum seekers at sea since October last year, but is due to finish in two weeks.

It will be replaced by a European border protection force that will have a third of the budget of the current operation.

The new force, Operation Triton, will stay close to the European coastline and has a purely surveillance role, rather than search and rescue far out to sea, as the Italians have been doing.

Amnesty International says it is "deeply alarmed" by the move.

According to the International Organisation for Migration, even with the massive Italian operation – which is costing the country more than $13 million every month – about 3,000 people have drowned trying to make the dangerous journey so far this year.

Thousands make dangerous journey from Libya coast

Sorry, this video has expired Italian Navy rescues asylum seekers from Mediterranean ( Sophie McNeill )

The ABC's Foreign Correspondent secured exclusive access on board an Italian navy ship, the San Giusto, as it roamed the southern Mediterranean searching for asylum seeker boats.

The boats generally launch from Libya, where the people smuggling trade is flourishing since the collapse of the government in 2011.

Over two days, the Foreign Correspondent team witnessed three dramatic rescues, two of boats full of young African men and another boat with hundreds of Syrian families.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Listen Duration: 3 minutes 32 seconds 3 m 32 s Italy says refugee rescue program can't continue Download 6.5 MB

Lamin, 22, from Gambia, the son of poor farmers, said he was sure he would find a better life in Europe.

"I have so many dreams I can't tell you," he said.

"We are going to try to get to Germany or the Netherlands," Syrian refugee Mohammad said.

Standing at Taranto train station in Italy's south, Mohammad and his family were allowed to walk out of an Italian immigration processing centre just hours after coming ashore on the San Giusto.

European Union law says refugees must seek asylum in the first country they arrive in, but in reality many of the so-called 'migranti' rescued by Italy try to leave the country as soon as they get to dry land.

With Italy still in the grip of recession with high unemployment, many of those brought ashore try to sneak over the Italian border to a more prosperous European country like Germany, Sweden or the Netherlands.

And Italy does not try very hard to stop them.

Critics say Italians encouraging people to risk their lives

Sorry, this video has expired Child asylum seekers rescued by Italian Navy in Mediterranean ( Sophie McNeill )

Switzerland has called on Italy to comply with its obligations and register all its asylum seekers.

Justice minister Simonetta Sommaruga said Switzerland could help share the burden, but Italy had to obey the rules.

Other European countries have also complained to the European Commission about Italy's inaction.

Operation Mare Nostrum started last October after a boatload of Eritreans sank within sight of the Italian island of Lampedusa, and at least 350 people died.

The disaster led to the Italians launching the search and rescue service, but it has been controversial.

There has been a tripling in the numbers of asylum seekers coming since 2013, and critics say the Italians are encouraging people to risk their lives.

But that is an accusation rejected by Vice Admiral Filippo Foffi, the Commander of the Italian Fleet.

"We have the duty in these cases when we are at sea, to intervene to save human life," Vice Admiral Foffi said.

"If we are not at sea then we can't see what happens, we can close our eyes, turn off the lights.

"There’s no need to 'turn back' the boats because they will die."

Migrant numbers rising 'due to increasing world conflict'

With more than half of the people rescued said to be from Eritrea and Syria, Vice Admiral Foffi said the numbers were on the rise due to increasing world conflict.

"There is a need to intervene at the origins of the problem before this horrible journey," he said.

After bearing the full costs of the operation for more than a year without any help from Europe, Vice Admiral Foffi said Italy's loose border controls had allowed many of those rescued to leave the country illegally.

"Perhaps the controls that are carried out to avoid these types of escapes are not rock solid," he said.

"But you must also think that one country only cannot be the holding place of these never-ending arrivals."

There are believed to be between 500,000 and 700,000 more people waiting in Libya to try to get to Europe.