It is the fruit trucks that are most rigorously checked. They typically carry crates of watermelons.
Piled on top of each other, they are, the authorities say, a classic place for immigrants to hide.
One of the vehicles pulls up at Patras port. The customs officers spring into action, cutting holes in the cardboard boxes to check the fruit, clambering inside to prod and search and shining torches underneath. After a lengthy process, the truck is cleared to board the ferry.
Patras is one of Greece's biggest ports - known as the gateway to the west. Ships here leave to Italy and the vehicles on board often travel further still. It is a smugglers' hub into Europe - one of the continent's most vulnerable borders.
Suddenly there is a commotion in one corner. The guards have opened a vehicle containing gas canisters. And five men are found crammed inside. They sit, heads bowed. One says he is from Afghanistan.
The driver is taken to be questioned by the prosecutor. As officers enter the vehicle one of the migrants falls to the floor, crying uncontrollably. A guard hands him water and tries to calm him.
"They will now be searched to see if they have relevant papers," says Evangelos Tasntzalos, the regional coastguard commander.
"Then they'll be ordered to leave the country - and while they're waiting they won't be allowed in Patras or in the other big port, Igoumenitsa."
More than 1,500 illegal immigrants were caught in Patras last year; every vehicle carrying them was impounded.
But while the port authorities are rigorous in their checks, plenty more migrants will attempt the journey. Over 80% of those entering the European Union now pass through Greece.
The typical route is in through the north-eastern corner of the country, across the Evros river from Turkey. They continue through Athens and down to Patras, in limbo until they pick what they hope is the right time to leave.
"I'm scared I'll die at any time because it's so unsafe here," one Afghan says while cowering on a disused railway track. "Nobody looks after us - there are no human rights in Greece. My dream is to go to England and I'll try every day to get there."
The influx of new arrivals here has made immigration a hot social issue and a key theme in the upcoming election. In last month's inconclusive poll, the virulently anti-immigration Golden Dawn party swept into parliament for the first time in its history, promising to lay landmines along the border with Turkey.
The party rejects the neo-Nazi label, but its leader has been filmed making Hitler salutes, and he recently denied that gas chambers were used in the Holocaust and said the figure of six million Jews killed was "an exaggeration".
During a heated TV debate on Thursday a party spokesman hit a woman MP in the face, prompting a warrant for his arrest.
Last month, Golden Dawn members rounded on a derelict factory in Patras traditionally used by immigrants for shelter. They threw petrol bombs and set fire to parts of the building, clashing with riot police. The incident was sparked by the murder of a Greek man, allegedly by three Afghans.
The victim's cousin, Thymios Koklis, says the attitude of Greeks towards uncontrolled immigration is hardening.
"We can't have so many immigrants - we don't even have jobs ourselves," he says. "The migrants are in a way the victims of this whole story. But I would blame the government that doesn't do anything to protect Greeks from the hordes who come here. We're very scared of them - people say they would take the law into their own hands."
Would he take the law into his own hands?
"If the state can't protect me, someone has to. Myself and my family," he says.
Migrants now steer clear of the factory, leaving behind bits of soiled clothing and empty food packaging - the remnants of past lives strewn across the decaying floors. The building is a vast and squalid labyrinth - bits of Arabic graffiti are scrawled on the walls, shards of mangled concrete lie hanging and the place has a dank smell. There is even excrement in some corners.
Charities working on the issue say Greece must do more to help the vulnerable - and wake up to the bubbling tension.
"I feel ashamed when I see how immigrants are treated," says Haralambos Tabakis from the immigration group Praksis. "This is not the right way to deal with the issue. Greeks have been migrants for many years - we have left to Europe, the US, Australia: we would never have liked to be treated in this way. We know what migration is all about."
As dusk falls, the hidden migrants of Patras come out to line the waterfront, gazing across the ocean to a new life. As they wait here, the immigration issue grows ever more volatile.
They came to this troubled country with dreams of Europe. But Greece is sinking further into crisis and the mood here is darkening - on all sides.