In secret; in a clandestine manner.
Hugger-mugger, which is found in early citations in many different spellings - hucker-mucker, hoker-moker, hocker-mocker etc., is now archaic and is rarely heard, despite its previously common use as a noun, adjective and adverb:
Noun - Secrecy; the practice, or policy of keeping secrets.
Adjective - Operating in a way so as to ensure concealment, e.g. as cloak-and-dagger.
Adverb - By stealth; under cover.
The earliest known usage is as an adverb, in John Skelton's Magnyfycence, 1520:
"Thus is the talkyng of one and of oder As men dare speke it hugger-mugger."
The source of the phrase is unknown. Reduplicated phrase like hugger-mugger often have an active word which supplies the meaning and a rhyming secondary word which adds emphasis, for example, okey-dokey and lovey-dovey. This expression differs from those in that hugger and mugger have the same meaning, i.e. concealment. That said, the words were rarely used apart even in the Middle Ages and it is quite possible that whichever was coined second came via the reduplicated form.
It may be that the coinage of hugger-mugger was influenced by the earlier phrase hucker-mucker, which has the same meaning. This is known from the 15th century onward, for example, in the Paston Letters, 1461:
"He and hys wyfe and other have blaveryd here of my kynred in hoder-moder."
See other reduplicated phrases.