The parties were yet to make their first appearance and Worksafe declined to name them as they have the right to seek name suppression, a WorkSafe spokeswoman said.
She also refused to detail the nature of the charges, the number, or when they were laid.
The parties will appear in March.
Discoveries Educare is owned by a husband and wife team who own a dozen of the centres across Auckland. A week before the incident the pair won Westpac's best emerging business award.
Immediately after the incident the centre had its licence reduced to provisional while the Ministry investigated, but it has since been reinstated.
The wife told the Weekend Herald she "couldn't comment on anything at this stage". Her lawyers had been dealing with Worksafe, she said.
The husband previously told the Herald the incident was "horrible" and that he held concerns about the tree after it lost all its leaves. The couple apologised to parents at the time, reporting the children wouldn't have "lasting effects".
"We take our responsibility caring for our children extremely seriously. We pride ourselves on our safety record, and all our centres comply with appropriate health and safety regulations," a statement released at the time said.
The land is owned by another party and the daycare owner said he had informed tenancy agents of his concerns but didn't believe it posed a danger: "(It was) never in our dreams it would fall," he said at the time.
Auckland Council compliance manager Steve Pearce said trees on private property were the responsibility of land owners and it had no record of complaints in relation to the tree.
After the incident the Ministry of Education conducted its own investigation and issued a provisional licence to the centre while it reviewed other potential hazards.
A full licence was reissued on November 25 last year, two weeks after the incident, after it was "satisfied" with the information provided, the Ministry's deputy secretary of sector enablement and support Katrina Casey said in a statement.
"Besides out initial contacts with the centre and families following the incident, we had had no further contact. We also thought it was wise to issue warnings to schools and learning centres about environmental hazards on grounds and to check trees on sites and if necessary, consult an arborist.
"This was placed in our internal publications that are distributed to all learning centres and schools, and we also updated our website. It is vital to the operation of any learning environment to ensure the safety of children."