In the middle of the MV Cape Ray's cavernous car deck stand two large white tents. With their interior lights casting eerie shadows of the constant activity within, they look like twin crime scenes. But the commanders, crew and scientists on board the US ship hope they will prove to be just the opposite – a site where future crimes can be prevented.

The tents house two highly unusual contraptions, custom-built to neutralise the most dangerous of Syria's extensive stockpile of chemical weapons. Each looks like a mass of pipes, tubes and valves leading to and from a cylindrical container about the size of minibus, all contained in an L-shaped steel frame.

It is called a field-deployable hydrolysis system (FDHS) and it renders lethal chemical weapons virtually harmless by the simple expedient of adding hot water, which irreversibly alters the lethal agents' molecular composition. But it can only do that when the chemicals actually arrive. The 648ft grey hulk of the Cape Ray has been moored alongside Spanish warships at the Rota naval base near Cádiz for nearly two months, waiting.

According to a timetable laid down last year by the Organisation for the Prohibition of Chemical Weapons (OPCW) and endorsed by the UN security council, about 1,300 tons of chemical weapons and their precursors were supposed to have been taken off Syrian territory in January and put on two Scandinavian freighters anchored at the Syrian port of Latakia.

The Danish Ark Futura and the Norwegian Taiko are still there, but so far only 54% of the total stockpile has been loaded. Damascus says much of the delay has been caused by the eruption of fighting in the civil conflict. Latakia itself has come under rocket attack, most recently last month, but OPCW officials said operations there resumed on Thursday.

The Cape Ray is supposed to deal with about 560 tons of the most dangerous substances: a sulphur mustard blistering agent and DF, a precursor of the sarin nerve agent. However, only 43% of those "priority one" materials have so far arrived in Latakia. The rest, along with less menacing "priority two" chemical compounds, ingredients for Bashar al-Assad's chemical arsenal, are still scattered around Syria in military bases, but have been consolidated from 17 different locations at the start of the OPCW-brokered process late last year, to five now.

Contractors work on the the field-deployable hydrolysis system onboard the Cape Ray. Photograph: Jim Watson/AFP/Getty Images

The 30 June deadline for the entire Syrian arsenal to be destroyed is beginning to look seriously in doubt. The deadline was set down by the security council in a rare moment of unanimity following the deaths of over a thousand people in chemical weapons attacks last August. A UN investigation has found the weapons used appeared to match those in the Assad regime's arsenal.

Syria's government says almost all the remaining chemical weapons and precursors will be delivered to Latakia on 13 April and the material at the last, most precariously located, site will be delivered towards the end of the month.

"The Syrians are in control of the timeline. They have committed most recently that they will deliver the chemical weapons to Latakia no later than 27 April. We would like to see them meet that commitment," Rear Admiral Robert Burke, director of operations at US naval forces in Europe and Africa, told the Guardian.

"Regardless of when they're ready, we are ready now on the Cape Ray … After we get the chemicals, we project it will take approximately 60 days for the neutralisation process. That will go plus or minus a couple of days depending on weather."

All the priority one materials are to be loaded onto the Danish ship, the Ark Futura. As soon as it is full, it will sail for Italy, as will the Cape Ray from the opposite direction. The two will meet at the Italian port of Gioia Tauro, near the country's southern toe, and back up to each other like giant, mating sea creatures. This is so the steel casks contain the Syrian chemicals can be transferred outside Italian waters.

The Cape Ray will sail into the open Mediterranean, where the L-shaped contraptions on the main vehicle deck will start operating. The HD sulphur mustard and DF sarin precursor will be pumped into the hydrolysis systems – probably the most dangerous part of the process. To minimise the risk the entire deck will be depressurised – steel air locks have been added to its hatches and gangways – so that air can flow in in the event of a breach, rather than gases flow out.

The white tents will also be under negative pressure as an added precaution. Emergency decontamination equipment is on standby in the antechambers of each tent in case of accidents.

"Getting out of here, for a chemical molecule, will be like getting out of a maximum security prison," said Michael Luhan, the OPCW spokesman.

The Maryland-based scientists on board, from the Edgewood Chemical Biological Center, insist the technology – a scaled-down version of the equipment used in the late 1990s to destroy the US's chemical stockpile – is tested. During the operation the Cape Ray will circle in the Mediterranean, guarded by a flotilla provided by over ten countries.

Since the rift with the west over Ukraine, Russia is not longer prepared to be part of that flotilla, but has continued to offer naval security for the Scandinavian ships in Syrian waters.

The waste from the hydrolysis will be acidic, and will be put in titration tanks with caustic chemicals to raise its pH. The resulting effluent will be similar to much industrial waste being shipped around the world's oceans every day.

Once the hydrolysis is complete, the Cape Ray is to due to sail on to Ellesmere Port, where about 150 tons of effluent from the DF precursor will be unloaded for incineration by the French-based environmental services corporation Veolia. The waste from the sulphur mustard agent will be taken to Germany for incineration . The 500 tons of priority two chemicals will be transported by the Taiko straight from Latakia to Finland and then Port Arthur in Texas.

"We will work hard to meet the 30 June 30 deadline but that depends on when the Syrians deliver," Burke said. "What we won't compromise on is safety."