In 2006 the BBC was found to have a pro-EU bias by a report commissioned by itself:

The report may conclude that direction does not come from the Top but the problem is that the ‘troops’ are the ‘believers’ in the EU and they are the ones who mold the tone and direction of any programme as admitted by the report:

We were also told by Helen Boaden, the BBC’s former director of news admitted in July 2013 that:
The BBC has a “deep liberal bias” and has failed to reflect the public’s growing concerns about immigration and the European Union.
Seems nothing has changed.
The Spectator looks again at revelations that the BBC has pocketed money from the EU despite its claims to be ‘independent’ of politics:
Over the last three years the BBC has secretly obtained millions of pounds in grants from the European Union. Licence fee payers might assume that the Corporation would have been compelled to disclose the source of this money in its annual reports, but they bear no trace of it specifically. In the latest set of accounts, for example, these funds are simply referred to as ‘other grant income’.
Instead of making an open declaration, the BBC’s successful lobbying for this money had to be prised out of it using a Freedom of Information (FoI) request lodged for The Spectator, proving that there was never any danger of the state broadcaster’s bosses volunteering it willingly.
The FoI response confirms that BBC staff applied for, and accepted, about £3 million of EU funds between April 2011 and November 2013, most of which has been spent on unspecified ‘research and development’ projects, with the remaining £1 million spent on programming.
Rob Wilson MP, says:
‘The whole point of the licence fee is to protect the BBC’s political independence and impartiality by providing it with a source of funding that is outside the hands of governments and politicians. Thanks to this FoI response, we now learn that it has been going cap in hand to the EU for millions of pounds on the quiet over the last few years. Such outrageous flouting of the principles on which the BBC is based and funded will only promote cynicism about its political impartiality and lead to a loss of trust in the BBC’s independence.’
But it isn’t just the money…the BBC has been sidelining Labour MPs who are Eurosceptics so as to present ‘Euroscepticism’ as a rightwing plot:
When Newswatch [a site that checks for BBC pro EU bias] provided oral evidence [Of the BBC’s lack of reporting of Labour scepticism] to the House of Commons European Scrutiny Committee in March 2013, Labour MP Kelvin Hopkins said that the figures gathered by Newswatch were ‘a revelation’ to him as a Labour withdrawalist, and added: ‘Even in the House of Commons, at least one in 10 speeches are made by Labour withdrawalists, so the imbalance is very clear.’
Eurosceptic Labour MP Kate Hoey, now part of an unofficial coalition of politicians overseeing the privately-funded organisation Newswatch, which monitors the BBC for EU bias at a cost of £60,000 per year, says the FoI disclosure is ‘shocking’. She says:
‘I have grave concerns about the bias of the BBC when it comes to EU matters. I find the whole thing shocking. The lack of transparency is unjustified. Why does it seem so worried about people knowing where it gets its money? What has the BBC got to hide other than knowing that many of us don’t trust them on EU matters and the need for a referendum on Britain’s EU membership?’
Ms Hoey adds that she has concerns that the BBC ‘very rarely’ reports Labour MPs’ views on Europe. She says:
‘Even Today in Parliament [on Radio 4] always tries to convey Tory splits on Europe, and this doesn’t help the perception of an EU bias. There are Labour MPs with strong views on Europe as well. It doesn’t help that the BBC very rarely reports these views.’