In all, there were 2.3 million Japanese Army troops prepared to defend the home islands, backed by a civilian militia of 28 million men and women. Casualty predictions varied widely, but were extremely high. The Vice Chief of theImperial Japanese Navy General Staff, Vice Admiral Takijirō Ōnishi, predicted up to 20 million Japanese deaths.(Giangreco 2009, pp. 121–124)
A study from June 15, 1945, by the Joint War Plans Committee("The Final Months of the War With Japan. Part III (note 24)". Central Intelligence Agency.) who provided planning information to the Joint Chiefs of Staff, estimated that Olympic would result in between 130,000 and 220,000 U.S. casualties of which U.S. dead would be the range from 25,000 to 46,000.
Delivered on June 15, 1945, after insight gained from the Battle of Okinawa, the study noted Japan's inadequate defenses due to the very effective sea blockade and the American firebombing campaign.(Carroll 2007, p. 48.)
Secretary of WarHenry L. Stimson was sufficiently concerned about high American estimates of probable casualties to commission his own study by Quincy Wright and William Shockley. Wright and Shockley spoke with Colonels James McCormack and Dean Rusk, and examined casualty forecasts by Michael E. DeBakey and Gilbert Beebe. Wright and Shockley estimated the invading Allies would suffer between 1.7 and 4 million casualties in such a scenario, of whom between 400,000 and 800,000 would be dead, while Japanese casualties would have been around 5 to 10 million.(Giangreco 2009, pp. 98–99.)(Frank 1999, p. 340.)
This second study has been largely questioned and is likely horribly trumped up.
Marshall began contemplating the use of a weapon which was "readily available and which assuredly can decrease the cost in American lives"( Giangreco 2009, p. 112)
Quantities of phosgene, mustard gas, tear gas and cyanogen chloride were moved to Luzon from stockpiles in Australia and New Guinea in preparation for Operation Olympic, and MacArthur ensured that Chemical Warfare Service units were trained in their use. Consideration was also given to using biological weapons against Japan.(Schaffer 1985, pp. 164–165.)
The US and allied forces were a far superior military force and could have easily combatted a group of under trained and poorly armed militia.
Japan's geography made the allied forces invasion plan obvious and in response the Japanese planned an all-out defense of the main island of Kyushu, leaving the other 3 for the most part defenseless.
tl;dr no, the civilian population was not even close to prepared to combat a full-scale invasion by allied forces.
You always hear claims of how, in an effort to avoid the necessity of a direct mainland invasion, the atomic bomb was used to encourage Japanese leadership to surrender (I understand this is it's own debate).