In the order yesterday, Jung told all senior officers that they would face strict action if they follow the orders of the city government which were declared "null and void" by the Centre.
Angry over the LG's order, Kejriwal in a letter to Prime Minister Narendra Modi said Jung should not have issued such an directive which created confusion in the administration when it was battling to contain the dengue menace.
Seeking Modi's intervention, Kejriwal said the issue can be sorted out two months later when the crisis subsides and that the Centre and the city government should now work closely to deal with the challenge of the mosquito-borne disease which is worst in the last five years.
The chief minister said Jung, in his order, has stated that the Centre has directed him to issue the directive and that he cautioned them of salary cut and other strict action if they do not follow it.
"I request both Prime Minister Narendra Modiji and the central government with folded hands that at this time, the people of Delhi are reeling under the menace of dengue, the disease has spread everywhere. The situation this time is worse compared to the last five years.
Slamming Jung, the Chief Minister said the order created confusion among the officers and will affect administration's efforts to tackle dengue.
"If the Centre wants to fight, it can do so two months later, when the crisis will subside. At least for two months, until the time dengue is in Delhi, they should not resort to such things and instead assist the government in fighting dengue.
"I urge you not to create confusion in the minds of the officers at this point and to let us work together as a team," Kejriwal said in the letter to Modi.
"Creating confusion does not suit the central government," Kejriwal told reporters.
Asked why LG has issued such an order, he said, "I have no idea as to what the motive is but at this point the government is fully focused on fighting dengue.