You have probably heard about the "Golden Week", exclusive to Japan.
There is 4 national holiday from April the 29th to May the 5th, so some japanese companies close during this week and employees could get this whole week off, which is quite a rare thing in Japan !
∴ 29th of April: the birthday of the Showa Emperor Hirohito
∴ 3rd of May: Constitution Day of Japan
∴ 4th of May: Greenery Day, celebration of nature
∴ 5th of May: Children's Day
The Golden Week is one of the longest vacation period of the year for many Japanese workers, and also, one of the busisest week of the year for japanese tourism sectors (with the New Year Period).
In all Japan, people could get around 1 week off, and the weather is quite good, so everyone travel at the same time, which is quite intense.
The 29th of April is the peak of departure. Airports are crowded, same for highways with a lot of traffic jam.
Hotels, flight, or other rental prices explode for the golden week, so people prepare their travel few month in advance. It is clearly not the best period to travel. It is important to book your hotels or rental-cars in advance if you plan to travel at this period if you have a limited budget, or if you prefer to have the choice between several options.
If you are free regarding your travel schedule, as my colleagues advised me, it is better to travel after the golden week done: prices are more affordable, and there is not so many tourist.