The system originally developed during 19 January as a weak tropical disturbance within the monsoon trough, to the northeast of the Santa Cruz Islands.

The cyclone made its closest approach to the island of New Caledonia on January 30; shortly after that, Beni weakened into a tropical depression.

The cyclone's heavy rains helped ease drought problems in Queensland; in fact, water reserves replenished five years worth of supply in one location.

[1][5] At around this time the JTWC initiated advisories on the system and designated it as Tropical Cyclone 12P, while it was located about 160 km (100 mi) to the south of the Solomon Island Rennell.

[4][6] After being named Beni executed a small clockwise loop for two days to the southeast of Rennell, partially as a result of a strong surface ridge of high pressure to the south of the low level circulation center.

[2] Environmental conditions surrounding the system also fluctuated during 25 January, as a result of Beni's position to the north of the strongly diffluent flow on the northern side of the upper-level ridge axis.

[1][3] Over the next two days conditions continued to fluctuate with shear playing a significant role in holding back further intensification of the system.

[1][4] Throughout 28 January Beni continued to intensify before the JTWC reported early the next day that the system had peaked, with 1-minute sustained wind speeds of 230 km/h (145 mph) which made it equivalent to a category 4 hurricane on the SSHS.

[7] Later that day RSMC Nadi reported that Beni had explosively developed and peaked as a Category 5 severe tropical cyclone on the Australian scale, with 10-minute sustained winds of 205 km/h (125 mph).

[1][4] At this time the system was moving to the southeast and was located about 400 km (250 mi) to the west of Port Vila, Vanuatu.

Rapid dissipating due to wind shear, the cyclone's central dense overcast was soon completely separated from Beni's center of circulation.

On 30 January, the storm passed south of New Caledonia and even closer to the commune of L'Île-des-Pins, but by this time, RSMC Nadi reported that Cyclone Beni was only a marginal Category 1 system with winds of 40 mph (65 km/h) and a pressure of 994 mbar (29.4 inHg).

[11] Saltwater inundation caused by strong waves damaged some garden plots, adding on further to the food shortage.

[15] In the Nouméa area, school holiday camps were closed and military personnel were sent to the Loyalty Islands in advance.

[9] Supermarkets in the area stocked up extra supplies and equipment to prepare for Beni to better support evacuees and those sheltering.

[23] Although far from Australia at that time, storm cells from Beni produced gale–force winds would periodically form and affect areas of southeastern Queensland on February 2.

[25] Runoff on the Fitzroy River caused by Cyclone Beni resulted in a moderate flood with an estimated return period of four years at Rockhampton.