"Undercutting Europe's climate and energy strategy is irresponsible," Mark Johnson, the World Wildlife Fund's senior policy advisor, told EurActiv, adding that the letter should be withdrawn.
"Europe should be using all of its powers to help Kosovo and its neighbours comprehensively on to a path towards eventual European integration," he said.
Lignite is a 'brown' form of coal which emits particularly high levels of CO2.
The letter, which is dated 19 May 2011 and signed by Energy Commissioner Günther Oettinger and Enlargement Commissioner Štefan Füle, pleads with the World Bank to maintain a partial risk guarantee (PRG) that it had offered to the 'Kosovo C' plant.
"We […] urge the Bank to continue its involvement in the New Kosovo Power Plant [NKPP] as the best and only way to improve Kosovo's environmental outcomes," it states.
'Kosovo C' would be less polluting than the existing 'Kosovo A' plant, the letter says, and so enable Pristina to meet its obligations under the Energy Community Treaty, and also to fulfil the requirements of the EU's Large Combustion Plant Directive, a precursor of eventual membership.
The EU's Energy Community includes Moldova, Ukraine and all the Western Balkan nations as contracting parties.
The Large Combustion Plants Directive aims to control emissions of sulphur dioxide, nitrogen oxide and dust from Europe's heavy industry.
This is an issue for Kosovo, a potential EU candidate, not least because the EU is its main trading partner.
"Should the Bank withdraw from the NKPP, we foresee the risk that Kosovo would renounce on its commitment to close 'Kosovo A' by 2015 and move to prolong the lifetime of the power plant," the two commissioners argue.
The Commission "has argued forcefully for the closure of the plant which can never conform to EU standards," it adds.
But environmentalists disagree.
According to Johnson, the 'Kosovo C' plant would put Pristina on "a divergent path" away from EU membership. It also contributed to a pattern of new coal generation being pushed outside the EU's external borders, from countries such as Italy and Poland, into those such as Albania and Belarus.
"New coal built outside the Union doesn't have to pay the price of carbon inside the EU," he said. "That carbon leakage triggered by pollution pricing is a growing concern for us."
Green MEP Bas Eickhout agreed, saying that he hoped the letter would not be a "prelude to Commissioner Oettinger's forthcoming energy vision for 2050".
"If we are creating an emissions trading scheme for the EU and at the same time creating high-carbon competitors just outside it, we are not only encouraging Kosovo to take the wrong environmental and economic direction, but also undermining our own low-carbon economies," he told EurActiv.
A European Commission spokesperson contacted by EurActiv was unable to comment.
The EU letter came a month after divisions emerged in the World Bank over plans to restrict funding for coal plants.
In 2010, a ferocious battle was fought between environmentalists and the Bank's board over plans to finance a South African coal plant with $3.75 billion of loans, which were eventually approved.
Within the EU though, funding subsidies to lignite coal plants have already proved controversial, due to the obstacle they pose to meeting the EU's goal of an 80-95% CO2 emissions cut by 2050.
The European Bank of Reconstruction and Development (EBRD) and European Investment Bank (EIB) are together providing €770 million of loans to a lignite coal plant in Sostanj, Slovenia.
The EIB argues that the Sostanj project will lead to a 28% reduction in carbon intensity, relative to the units it will replace.
But in their letter, the two commissioners merely cite a World Bank study which posits that closing 'Kosovo A', rehabilitating 'Kosovo B' and bringing 'Kosovo C' online would be "carbon neutral", meaning it would not change Kosovo's overall CO2 emissions.