The volume of containers through Shanghai, the world's busiest container port, fell 4.7 percent to 2.44 million TEUs from 2.56 million TEUs in May, the South China Morning Post reported.
Shanghai's cargo throughput fell 4.95 percent to 35.97 million tonnes from 37.85 million tonnes in May.
The container throughput in Shenzhen, the mainland's second-busiest port, fell 1.4 percent to 1.91 million TEUs from 1.93 million TEUs in May, after three consecutive months of increases to May.
Shenzhen's cargo throughput fell 1.3 percent to 18.74 million tonnes from 18.99 million tonnes in May.
"The global recovery has reached a turning point as the momentum provided by the inventory cycle wears off," Melissa Kidd wrote in a report for Lombard Street Research, a London economic think tank.
"Recent falls in the BDI (Baltic Dry Index), with weakening hard commodity demand in China and softening global data, point to a slowing down in the global recovery."
But, Charles de Trenck, an analyst at consultancy Transport Trackers, pointed to the double-digit year-on-year growth, as opposed to the month-on-month figures, of the Shanghai and Shenzhen ports in June.
"These are not bad numbers," de Trenck said.
Shenzhen's container throughput grew a sizzling 35.2 percent year on year last month, while Shanghai's container throughput growth was 21.4 percent year on year.
However, he predicted slower growth for the mainland's port throughput in the coming months, because retailers in the United States were likely to slow down their inventory restocking.
One of the problems facing shippers, de Trenck said, was a shortage of containers that could grow more acute if container volumes continued to rise in the peak season.
He said the liner industry thought the shortage "was going to be solved, but it could last the whole summer".
Part of the problem has been caused by container lines cutting the speed of their ships to reduce fuel consumption and increase available capacity, resulting in containers kept on board ships at sea for longer.
Asian shippers groups estimated the slow sailing had reduced the number of containers available by about 20 percent. Container liners cannot easily "change their schedules around" either by increasing the speed of their ships or withdrawing ships from service, de Trenck said. This is because most carriers are in alliances with other shipping lines and each contributes vessels or deck space to each route or service.