Earlier, the ministry clarified his comments, noting he had also said there could only be a political solution.
Meanwhile, the US has agreed to send Patriot missiles to Turkey.
Defence Secretary Leon Panetta signed orders to deploy two batteries and 400 military personnel along the border with Syria to defend Turkish civilians against attacks by missiles or aircraft.
Germany and the Netherlands are also sending two batteries each to southern Turkey. All six will be placed under the command of Nato and are scheduled to be operational by the end of January.
On Wednesday, it was revealed that the Syrian military had resorted to firing Scud ballistic missiles at rebels in an attempt to slow their advance.
Mr Bogdanov’s assessment of the situation in Syria appeared to signal a major shift in the diplomatic stance of Russia, which has remained a staunch ally of President Bashar al-Assad since the uprising began in March 2011 and blocked attempts at UN Security Council action.
Mr Bogdanov reiterated Russia’s principle position – that there is no alternative to a political resolution in Syria ”
“We must look squarely at the facts, and the trend now suggests that the regime and the government in Syria are losing control over more and more territory,” the deputy foreign minister said on Thursday.
“Unfortunately, it is impossible to exclude a victory of the Syrian opposition,” he added.
Mr Bogdanov’s words were reported by the leading Russian news agencies, but Russian TV channels did not broadcast them and the foreign ministry did not publish them on its website.
The US later commended Russia for “waking up to the reality”.
On Friday, the Russian foreign ministry said Mr Bogdanov had “issued no statements and given no special interviews in recent days”.
The BBC’s Steve Rosenberg in Moscow says that is technically true, as his comments were made during a panel discussion in Moscow.
“At the discussion on the Middle East and North Africa at the Russian Public Chamber, Syria was discussed,” a ministry spokesman said.
“The well-known claim of the Syrian opposition and its external sponsors predicting ‘a quick victory over the authorities in Damascus’ was quoted,” he added. “In this context, Mr Bogdanov reiterated Russia’s principal position – that there is no alternative to a political resolution in Syria based on the Action Group for Syria, agreed in Geneva on 30 June.”
In other words, our correspondent says, the foreign ministry claims that Mr Bogdanov did not go off message, even though phrases like “facts should be faced” and “the victory of the Syrian opposition cannot be excluded” suggest otherwise.
Even if this is not the Russian government’s official public position yet, Mr Bogdanov’s comments indicate what Moscow is really thinking, he adds.
The Action Group for Syria called for an immediate cessation of violence and the establishment of a transitional government that could include officials serving under President Assad and members of the opposition.
In a separate development on Friday, the UN’s humanitarian chief, Valerie Amos, said it would try to maintain its aid operations in Syria and ensure relief supplies were stockpiled in neighbouring countries
“We all have staff who are still on the ground, of course we will continue to look at the safety and security of our staff, but our commitment is to keep our operations going,” she told reporters in Geneva.
The UN believes up to four million people inside Syria will need humanitarian aid by early next year, up from 2.5 million. Another 500,000 Syrians have also fled to neighbouring countries.