Operations to secure Europe's frontiers face potential cutbacks in order to finance extended patrols in the Mediterranean in the wake of a series of migrant deaths, including the apparent murder of around 500 people by traffickers, the EU's borders agency says.

Frontex says it faces a shortfall of €2.3m (£1.8) after extending operations off Italy, which were due to finish this month, until the end of November; this is a significant sum for an already hugely stretched organisation with an annual operational budget of just €42m.

The operation, covering waters to the south of Sicily and the Pelagie islands – among them Lampedusa, a common landing point for migrant boats from Africa – involves planes and crew provided by the Netherlands and Spain but is paid for by Frontex, and has already cost €13m this year. When the Dutch and Spanish mission finishes at the end of September they will be replaced by aircraft from elsewhere in the EU, something the agency says could affect operations elsewhere.

"Because of the situation in the central Mediterranean we have decided to extend the operation, for the moment until the end of November," said Izabella Cooper, a Frontex spokeswoman. "It means we need additional money, and we're at the end of the year and, obviously, all operations are planned well in advance. We're looking at reallocating money from other operations that we run."

Frontex, which coordinates border security among EU nations rather than having assets of its own, has a series of other similar operations to monitor and control migrant arrivals, including three in Spain, two in Greece and one in Bulgaria. Cooper said: "We obviously have to maintain the operational presence in other places, but we're shifting the financial resources to the central Mediterranean, so we can extend the operation."

There is little scope for savings, she said: "You have Spain, where the migratory pressure is also big, you have Greece, where it's the same. But then there's Italy."

The Frontex decision is not directly connected to the news on Monday that up to 500 people, including between 50 and 100 children, were feared drowned after traffickers rammed and sunk their boat midway on a voyage between Egypt and Malta. But it comes amid a wider pattern of massively increased numbers sailing to Europe this year, the majority joining boats along the relatively lawless coasts of Libya.

A total of 120,000 migrants have arrived by sea in Italy so far in 2014, mostly following rescue operations. As well as the Frontex efforts, the Italian navy has run a much larger operation for the last year, called Mare Nostrum, which was set up following the deaths of hundreds of migrants in October last year when their boat caught fire and capsized just off Lampedusa. However, the operation costs around €9m a month, a burden Italy is understandably keen to share among other EU nations.

Frontex is currently in talks with Italy over a planned new operation called Triton, which would help to absorb some of the pressure, but would also require the European Commission to give the agency a notably increased budget.

"What is sure is that we will not replace Mare Nostrum as such," said Cooper. "We are discussing very closely with the Italian authorities how we can provide more support to them within our mandate and within our possibilities – we do not have assets on the scale of the Italian navy."

While Frontex's mandate is border control rather than search and rescue, she added, in the Mediterranean the two ended up being the same thing: "In every maritime operation you have the obligation of saving lives. Most of these boats are in distress. The traffickers put people on these unseaworthy, rusty fishing boats that shouldn't be in the sea at all, let alone with 650 people on board."

The UN refugee agency, the UNHCR, is also warning of the need for other European nations to assist Italy, and to a lesser extent Greece, in coping with the flow of migrants. "The rescue-at-sea efforts can't just be the responsibility of these two countries. We've been advocating for a more concerted European effort to help with this," said Andrej Mahecic, a UNHCR spokesman.

The UN agency said the usual peak summer "sailing season" was expected to last well into October this year, such was people's desperation, plus the opportunities provided by the chaos in Libya. Mahecic said: "With the situation in Libya, how volatile it is at the moment, there is perhaps less control of the border, and there are many people who simply fear they can't stay any longer. They opt to board boats leaving Libyan shores."