I am not sure if this correct, but here is how I can explain it, from what I gather from the people I know.
Tokyo's Olympic bid was initiated by a former governor who was keen to do big things while ignoring some real problems like homeless people, unemployment etc. Most older people seem to think that Olympics is a nice-to-have but not really necessary given the current economic status. There is also public displeasure on overspending by both the government and the civil service. So, when the costs are larger than standard or planned, media is quick to jump on it.
The current Tokyo governor came to power after two governors who resigned on charges of bribery and unauthorised spending. She has been talking a lot about cutting costs, and this is her chance. She is quite popular at this point, but has not delivered anything yet.
Lastly, it has been common in the construction sector here to spend a lot and get things right, rather than cut costs. So,I can understand that everyone wants to estimate high on a big event like this.