The BND declined to comment on the report by Bild daily which comes as Berlin and other Western governments shun official cooperation with Syrian President Bashar al-Assad over his regime's abuses.
The mass-circulation daily, citing unnamed "informed sources", said BND agents had been travelling regularly to Damascus for talks with their Syrian counterparts and that the service wanted to reopen an office there.
The BND told AFP that it only informs the government and a parliamentary oversight panel of "operative aspects" of its work, and a spokeswoman for Chancellor Angela Merkel also declined comment at a press conference.
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Bild said the aim of the contact was to exchange information on Islamist extremists and to open a channel of communication in the event of any potential crisis, such as a German Tornado pilot being shot down over territory held by jihadists.
Germany has deployed Tornado surveillance aircraft and other non-combat military support to the US-led coalition fighting the Islamic State group, which controls wide areas of Syria and Iraq.
Merkel has argued the world must seek a diplomatic solution to the Syrian conflict to end the killing there, to better focus on fighting IS, and to reduce massive refugee flows to Europe.
But she has repeatedly stressed that this must not include cooperation with Assad, who, she said, "keeps dropping barrel bombs on his own people", and whose regime was the main cause of the refugee exodus.