There is controversy over the Environmental Impact Assessment (EIA), which “does not contain adequate information on the seismic conditions, nor does it address beyond design basis accidents or give details of the potential impacts of decommissioning”. Furthermore, following legal action by environmental groups, the authors of the original EIA confirmed, in court, that it was flawed and would require a new EIA once a designer and builder were appointed. The total cost of the project is now estimated by the operator to be around €7 billion (€4 billion for the power stations plus associated infrastructure development costs).

Environmental organizations Greenpeace, Friends of the Earth (Europe), Urgewald, Bankwatch, World Information Service on Energy and the Bulgarian NGO BeleNE! oppose the plant's construction, and have expressed the following concerns:

• negative effect on the tourist industry and the agriculture of northern Bulgaria
• safety concerns over the use of nuclear technology
• location in a seismic active zone
• the expense of the project
• risk of terrorist attack
• problems with the transportation, procession and preservation of the nuclear waste
• complete unnecessity of further nuclear power in the first place, as better options are available.

Concerns regarding the construction of the plant have mainly been felt in nearby Romania, with articles in the newspapers such as Cotidianul, România Liberă and Ziarul even going as far as comparing the project with Chernobyl despite a new generation of VVER reactors is to be used, and not the cheaper graphite-moderated RBMK series like Chernobyl's.

Critics say the project is economically flawed, open to corruption and mismanagement, and will cement Russian dominance of Bulgaria's energy sector.

On June 11, 2010, the Bulgarian government announced that it would freeze indefinitely the planned construction of the Belene nuclear power plant because it was uncertain when the investment would be returned. Five months later, on December 2, a non-binding memorandum of understanding was signed between NEK EAD, Rosatom, Altran and Fortum, setting up a 6.3 bln. euro price on the power station, after months of unsuccessful talks on the cost and redeemability of the project itself. Further disagreement and the persistent demands of the Bulgarian government to lower the cost under 5.0 billion euro led to the termination of the project in March 2012. However, in late 2012 the opposition initiated a referendum petition which was signed by 1,385,283 people and the first national referendum in the history of modern Bulgaria was held on January 27, 2013. A majority of the people had voted ′Yes' but despite that, the number of voters who attended the voting was too low for it to pass. The referendum passed the question further to the Parliament, which decided on 27 February 2013 to suspend it. Later on 30 May 2013 the newly elected Cabinet Prime Minister Oresharski announced there is a possible restart for it.

The negotiations stalled again after the GERB government decided to add an American or a European contractor to the project, as well as insisting for Atomstroyexport to lower the price to less than five billion euro. As no major European or American investor appeared, the talks continued to yield no results. This led to the official termination of the Belene project in March 2012. A thermal powerplant using gas from the South Stream pipeline will be built on the site, and the reactor for Unit 1 will be assembled as Unit 7 at the Kozloduy NPP.

In June 2016, the International Court of Arbitration awarded Atomstroyexport €620 million in compensation for equipment already manufactured for the plant, which will be delivered to Bulgaria following payment.

Although the project was cancelled by parliament, the Bulgarian Socialist Party government of Plamen Oresharski (elected in May 29, 2013) has spoken publicly about restarting the project.

In 2016 discussions took place with Rosatom about the possibility of installing one of the reactors at Kozloduy Nuclear Power Plant and selling the second one to a third party. An alternative is a privately financed completion of Belene.

On 7 June 2018, the Bulgarian Parliament voted to abolish the moratorium on the construction of the power plant. The aim of the government is to complete the project through funding by a strategic investor, what interest has so far been declared by several companies. Minister of Energy should develop an investor selection procedure and propose options for structuring the project by 31 October 2018. According to the Minister, the plant can be completed within 7-8 years.

The AES 92 variant proposed for implementation at the Belene NPP site is a new generation VVER type reactor that has been licensed by regulatory authorities in Russia. It has been declared to meet all safety requirements as well as recommendations from the IAEA and INSAG and has been also confirmed by a special analysis of leading experts from EDF based on the recognized European Utility Requirements. This variant of the AES can make use of the two partially completed Belene NPP reactors started in the 1980s. The design directly uses a majority of the already built civil structures and facilities related to generic plant needs. Existing foundations and civil structures will be further evaluated with a view to incorporation into the new design.